Evolution in Mendelian Populations

Impact of complex spatial population structure on early and long-term adaptation in rugged fitness landscapes

We study how rugged fitness landscapes are explored by spatially structured populations with demes on the nodes of a graph, connected by migrations. In the weak mutation and rare migration regime, we find that, in most landscapes, migration asymmetries associated with some suppression of natural selection allow the population to reach higher fitness peaks first. In this sense, suppression of selection can make early adaptation more efficient. However, the time it takes to reach the first fitness peak is then increased. We also find that suppression of selection tends to enhance finite-size effects. Finite structures can adapt more efficiently than very large ones, especially in high-dimensional fitness landscapes. We extend our study to frequent migrations, suggesting that our conclusions hold in this regime. We then investigate the impact of spatial structure with rare migrations on long-term evolution by studying the steady state of the population with weak mutation, and introducing an associated steady-state effective population size. We find that suppression of selection is associated to small steady-state effective population sizes and thus to small average steady-state fitnesses.

Subcontinental genetic variation in the All of Us Research Program: Implications for biomedical research

The All of Us Research Program (All of Us) seeks to accelerate biomedical research and address the underrepresentation of minorities by recruiting over 1 million participants across the United States. A key question is how self-identification with discrete, predefined race and ethnicity categories compares to genetic variation at continental and subcontinental levels. To contextualize the genetic variation in All of Us, we analyzed ∼2 million common variants from 230,016 unrelated whole genomes using classical population genetics methods alongside reference panels such as the 1000 Genomes Project, Human Genome Diversity Project, and Simons Genome Diversity Project. Our analysis reveals that participants within self-identified race and ethnicity groups exhibit gradients of genetic variation rather than discrete clusters. The distributions of continental and subcontinental ancestries show considerable variation within race and ethnicity, both nationally and across states, reflecting the historical impacts of US colonization, the transatlantic slave trade, and recent migrations. All of Us samples filled most gaps along the top five principal components of genetic variation in current global reference panels. Notably, Hispanic or Latino participants spanned much of the three-way (African, Native American, and European) admixture spectrum. Ancestry was significantly associated with body mass index (BMI) and height even after adjusting for socio-environmental covariates. In particular, West-Central and East African ancestries showed opposite associations with BMI. This study emphasizes the importance of assessing subcontinental ancestries, as the continental approach is insufficient to control for confounding in genetic association studies.

The Patterson-Price-Reich's rule of population structure analysis from genetic marker data

Delineating population structure from the marker genotypes of a sample of individuals is now routinely conducted in the fields of molecular ecology, evolution and conservation biology. Various Bayesian and likelihood methods as well as more general statistical methods (e.g. PCA) have been proposed to detect population structure, to assign sampled individuals to discrete clusters (subpopulations), and to estimate the admixture proportions of each sampled individual. Regardless of the methods, the power of a structure analysis depends on the strength of population structure (measured by FST) relative to the amount of marker information (measured by NL, where N and L are the numbers of sampled individuals and loci respectively). Patterson, Price and Reich (2006) proposed that population structure is unidentifiable when data size D = NL is smaller than 1/FST2 and quickly becomes identifiable easily with an increasing D or FST when D>1/FST2. In this study, I investigated this phase change PPR rule by analysing both simulated genomic data and empirical data by four likelihood admixture analysis methods. The results show that the PPR rule is largely valid, but the accuracy of a structure analysis is also affected by the number of subpopulations K. A more complicated population structure with a larger K requires a larger NLFST2 to resolve accurately. For a given NLFST2 above the PPR threshold value of 1, increasing L and decreasing N is advantageous over increasing N and decreasing L in improving admixture estimation accuracy.

Spatial Replication Is Important for Developing Landscape Genetic Inferences for a Wetland Salamander

Habitat fragmentation is a pressing threat to wildlife populations, and maintenance of gene flow between populations is an essential goal of conservation. Resistance surfaces have emerged as an important tool for modelling connectivity and developing management strategies to mitigate effects of habitat fragmentation. However, recent studies have noted inconsistencies in the factors most strongly associated with connectivity across different landscapes. Thus, replication of genetic-based resistance surface optimisation across landscapes may be necessary for making robust conclusions about the influence of environmental variables. Accordingly, replication represents a substantive challenge and opportunity in the field of landscape genetics. In this study, we conducted replicated landscape genetic analyses across five landscapes in Tennessee and Kentucky for a threatened wetland amphibian, the four-toed salamander (Hemidactylium scutatum). We tested multiple hypotheses of how different landscape features that could directly affect small, desiccation-intolerant amphibians (e.g., canopy cover) influenced gene flow and assessed the appropriate scale at which to model different features. We found some concordance in the landscape features that influenced gene flow (e.g., a common importance of forest cover and topography), but also some differences-potentially owing to the difference in variability of predictors across landscapes. We also found discordance in the scale of effect of different features across landscapes. Our work emphasises that flat areas of moist forest not bisected by roads may be important for H. scutatum conservation, and our replicated design allows us to identify relationships that would have been missed if only using one study site.

The genetic structure and diversity of smallholder dairy cattle in Rwanda

Previous genomic characterisation of Rwanda dairy cattle predominantly focused on the One Cow per Poor Family (locally called "Girinka") programme. However, smallholder farmers in Rwanda have benefited from other livestock initiatives and development programmes. Capturing and documenting the genetic diversity, is critical in part as a key contribution to genomic resource required to support dairy development in Rwanda. A total of 2,229 crossbred animals located in all dairy-producing regions of Rwanda were sampled. For each animal, a hair sample was collected and genotyped by using the Geneseek Genomic Profiler (GGP, Neogen Geneseek®) Bovine 50 K (n = 1,917) and GGP Bovine 100 K arrays (n = 312). The combined dataset was subject to quality control, data curation for use in population genetics and genomic analyses. To assess the genetic structure and diversity of the current population, key analyses for population structure were applied: Principal Component Analysis (PCA), population structure and diversity, admixture analysis, measures of heterozygosity, runs of homozygosity (ROH) and minor allelic frequency (MAF). A dataset of global dairy population of European taurine, African indicus and African taurus (n = 250) was used as reference. Results showed that Rwanda cattle population is highly admixed of diverse pure and crossbred animals with average MAF of 33% (standard error; se = 0.001) with proportion of foreign high yielding (taurine) dairy breeds of Jersey Island (18%); 12% non-Island Jersey and 42% Holstein-Friesian ancestries. Two African Bos taurus and five Bos indicus breeds contributed 28% of their genetics. Genetic distances were highest in Gir and N'dama (0.29); and Nelore and N'dama (0.29). There were 1,331 ROH regions and average heterozygosity were high for Rwanda cattle (0.41 se = 0.001). Asides well-established genes in cattle, we found evidence for a variety of novel and less-known genes under selection to be associated with fertility, milk production, innate immunity and environmental adaptation. This observed diversity offers opportunity to decipher the presence and/or lack of genetic variations to initiate short- and long-term breed improvement programmes for adaptation traits, disease resistance, heat tolerance, productivity and profitability of smallholder dairy systems in Rwanda.

Fast simulation of identity-by-descent segments

The worst-case runtime complexity to simulate haplotype segments identical by descent (IBD) is quadratic in sample size. We propose two main techniques to reduce the compute time, both of which are motivated by coalescent and recombination processes. We provide mathematical results that explain why our algorithm should outperform a naive implementation with high probability. In our experiments, we observe average compute times to simulate detectable IBD segments around a locus that scale approximately linearly in sample size and take a couple of seconds for sample sizes that are less than 10,000 diploid individuals. In contrast, we find that existing methods to simulate IBD segments take minutes to hours for sample sizes exceeding a few thousand diploid individuals. When using IBD segments to study recent positive selection around a locus, our efficient simulation algorithm makes feasible statistical inferences, e.g., parametric bootstrapping in analyses of large biobanks, that would be otherwise intractable.

Continued collaboration of ex situ and in situ programs is critical for the genetic sustainability of the endangered Rana pretiosa

Retaining sufficient genetic variation for both short and long-term sustainability is a chief aim of ex situ programs for threatened species. Conservation breeding and reintroduction programs exist but oftentimes little is known about the genetic variation of in situ or ex situ populations. We collected genetic samples from both wild and zoo populations of Canada's most endangered anuran, the Oregon Spotted Frog (Rana pretiosa) to compare genetic diversity (observed and expected heterozygosity), inbreeding coefficients (FIS), effective population sizes (Ne) and population structure using single-nucleotide polymorphisms (SNPs). We found low diversity in situ and lower diversity ex situ, with positive inbreeding coefficients indicating assortative mating in both wild and zoo populations. Ex situ breeding programs that allowed free mate choice retained more genetic variation compared to those where breeding groups were pre-determined. Mixed source zoo populations were less differentiated from their wild source populations than the latter were among themselves, indicating sufficient representation of wild populations in zoo populations. The patterns we uncover support continued collaboration of ex situ and in situ endeavours as supplementation will likely be required for the long-term viability of the very wild populations the zoos rely on for genetic sustainability.

Many-strategy games in groups with relatives and the evolution of coordinated cooperation

Humans often cooperate in groups with friends and family members with varying degrees of genetic relatedness. Past kin selection can also be relevant to interactions between strangers, explaining how the cooperation first arose in the ancestral population. However, modelling the effects of relatedness is difficult when the benefits of cooperation scale nonlinearly with the number of cooperators (e.g., economies of scale). Here, we present a direct fitness method for rigorously accounting for kin selection in n-player interactions with m discrete strategies, where a genetically homophilic group-formation model is used to calculate the necessary higher-order relatedness coefficients. Our approach allows us to properly account for non-additive fitness effects between relatives (synergy). Analytical expressions for dynamics are obtained, and they can be solved numerically for modestly sized groups and numbers of strategies. We illustrate with an example where group members can verbally agree (cheap talk) to contribute to a public good with a sigmoidal benefit function, and we find that such coordinated cooperation is favoured by kin selection. As interactions switched from family to strangers, in order for coordinated cooperation to persist and for the population to resist invasion by liars, either some level of homophily must be maintained or following through on the agreement must be in the self-interests of contributors. Our approach is useful for scenarios where fitness effects are non-additive and the strategies are best modelled in a discrete way, such as behaviours that require a cognitive 'leap' of insight into the situation (e.g., shared intentionality, punishment).

Recombinant inbred line panels inform the genetic architecture and interactions of adaptive traits in Drosophila melanogaster

The distribution of allelic effects on traits, along with their gene-by-gene and gene-by-environment interactions, contributes to the phenotypes available for selection and the trajectories of adaptive variants. Nonetheless, uncertainty persists regarding the effect sizes underlying adaptations and the importance of genetic interactions. Herein, we aimed to investigate the genetic architecture and the epistatic and environmental interactions involving loci that contribute to multiple adaptive traits using 2 new panels of Drosophila melanogaster recombinant inbred lines (RILs). To better fit our data, we re-implemented functions from R/qtl using additive genetic models. We found 14 quantitative trait loci (QTLs) underlying melanism, wing size, song pattern, and ethanol resistance. By combining our mapping results with population genetic statistics, we identified potential new genes related to these traits. None of the detected QTLs showed clear evidence of epistasis, and our power analysis indicated that we should have seen at least 1 significant interaction if sign epistasis or strong positive epistasis played a pervasive role in trait evolution. In contrast, we did find roles for gene-by-environment interactions involving pigmentation traits. Overall, our data suggest that the genetic architecture of adaptive traits often involves alleles of detectable effect, that strong epistasis does not always play a role in adaptation, and that environmental interactions can modulate the effect size of adaptive alleles.

Evolutionary divergence on the Qinghai-Tibet Plateau: How life-history traits shape the diversity of plateau zokor and pika populations

Understanding how species diverge and adapt is fundamental to unraveling biodiversity. While environmental impacts on species evolution are well-documented, the roles of intrinsic life-history traits remain underexplored. The Qinghai-Tibet Plateau, with its harsh conditions and unique biodiversity, offers a natural laboratory for such investigations. Here, we examined two sympatric small mammals-the solitary, low-dispersal plateau zokor (Eospalax baileyi) and the social, high-dispersal plateau pika (Ochotona curzoniae)-to elucidate how life-history traits shape population structures and adaptive strategies. Through whole-genome sequencing and cardiac-blood phenotype analyses, we reveal striking differences in their evolutionary trajectories. Despite enduring similar environmental pressures, plateau zokor populations exhibit pronounced genetic subdivisions, high inbreeding, and distinct local adaptations. In contrast, plateau pika populations display genetic panmixia, widespread diversity, and adaptive uniformity. Demographic inference highlights plateau zokors experienced severe population bottlenecks and restricted gene flow during glacial periods, underscoring the impact of dispersal capacity on evolutionary outcomes. Our findings demonstrate that intrinsic biological traits, particularly dispersal ability, fundamentally influence genetic architecture, population connectivity, and local adaptation. This study not only provides empirical evidence of how life-history traits shape evolutionary dynamics but also offers a framework for integrating intrinsic and extrinsic factors in understanding biodiversity formation.

DCMS analysis revealed differential selection signatures in the transboundary Sahiwal cattle for major economic traits

The Sahiwal are among the most prominent international transboundary dairy cattle distributed in large numbers between India and Pakistan. With the elapse of more than seven decades after the independence and limited cross-border exchange of Sahiwal germplasm, one thought-provoking question arises as to whether natural and artificial selection could alter the genomic signature patterns in the Sahiwal, reared for different purposes in these two countries. Deciphering the genetic mechanisms that underlie economic traits is essential for advancement and long-term breeding plans that are reflected in the distinct selection signatures they carry. To identify these genomic signatures, three medium-density SNP datasets of Sahiwal from three geographical locations of India and Pakistan were analyzed, using De-Correlated Composite of Multiple Selection Signals technique to identify the major candidate genes. In the genome of Sahiwal, a total of 70 genomic regions with 261 protein-coding genes were found. Milk production (NEK11, HMGCS1, BTN1A1,KCNH3), reproduction (SH3BGR, PSMG1, BRWD1,B3GALT5) and immune response genes (BPIFB1, MCOLN2) were more closely related to the Indian Sahiwal. Pakistani Sahiwal had genes closely linked with the dual-purpose meat (RALGAPA2, RIN2, CFAP61), and milk (SLC24A3 GALNT17, BACH2) traits. Our findings revealed differential patterns of selection signatures in transboundary Sahiwal cattle.

Substitution-Mutation Rate Ratio (c/µ) As Molecular Adaptation Test Beyond Ka/Ks: A SARS-COV-2 Case Study

The Ka/Ks ratio test, which assesses nonsynonymous versus synonymous substitution rates in Translated Region (TR) of a genome, is widely used to quantify fitness changes due to mutations but its critical limits are to be addressed. Ka/Ks can categorize the total fitness change as neutral (Ka/Ks = 1), beneficial (Ka/Ks > 1), or deleterious (Ka/Ks < 1), only if synonymous mutations are neutral. Otherwise, Ka/Ks only provides the fitness change due to protein sequence change. This neutrality assumption also renders this test inapplicable to sites in non-protein-coding UnTranslated Region (UTR). Our previous work introduced a substitution-mutation rate ratio (c/µ) per nucleotide site test (c: substitution rate in UTR/TR or a mean value of Ka and Ks in TR; and µ: mutation rate) as a generalized alternative to detect selection pressure, offering a broader application without forementioned presumptions. This paper derives a general equation linking c/µ with weighted Ks/µ and Ka/µ (c/µ = Ps*(Ks/μ) + Pa*(Ka/μ), Ps and Pa: proportions of synonymous and nonsynonymous sites under a mutation model and a codon table), demonstrating that Ka/Ks infers the same fitness change as c/µ does only if synonymous mutations are neutral (i.e. Ks/µ = 1). Otherwise, Ka/Ks might provide a different assignment from the c/µ test. Indeed, our comparative analysis of the c/µ and Ka/Ks tests across 25 proteins of SARS-COV-2 using three independent genomic sequence datasets shows that Ka/Ks inaccurately reports the type of fitness change for 7 proteins. Our findings advocate for the c/µ test to complement traditional Ka/Ks test to detect the selection pressure at a nucleotide site in a genome.

Shared Dispersal Patterns but Contrasting Levels of Gene Flow in Two Anadromous Salmonids Along a Broad Subarctic Coastal Gradient

Dispersal is a highly variable trait influenced by life history and ecological factors, affecting gene flow when dispersers successfully reproduce. Anadromous salmonids, with their diverse migratory strategies and ecological traits, serve as an ideal model for studying dispersal evolution, showcasing significant inter- and intraspecific variation. Although environmental factors like temperature likely influence dispersal propensity, their effects remain poorly documented. This study compares dispersal patterns and population structure in lake whitefish (Coregonus clupeaformis) and brook charr (Salvelinus fontinalis) along the subarctic coastline of James Bay, covering four degrees of latitude. These species differ in life history and population size, representing contrasting ends of a continuum influencing dispersal and gene flow. We hypothesised that lake whitefish, with shorter freshwater residency and potentially reduced olfactory imprinting, would disperse more frequently than brook charr. Using low-coverage whole-genome sequencing, we found that lake whitefish exhibited broader-scale population structure and greater long-distance dispersal capacity than brook charr. Surprisingly, both species showed similar dispersal rates and population differentiation levels. However, lake whitefish had effective population sizes approximately 10 times larger than brook charr, indicating that while their dispersal is common, it results in lower effective gene flow. Moreover, dispersal rates in both species were lower in the northern study area, likely due to colder temperatures, delayed ice break and shorter growing seasons. These findings yield insights into how life history and environmental variation shape dispersal evolution in migratory species.

Whole-genome sequencing reveals patterns of runs of homozygosity underlying genetic diversity and selection in domestic rabbits

BACKGROUND

Runs of homozygosity (ROH) are continuous segments of homozygous genotypes inherited from both parental lineages. These segments arise due to the transmission of identical haplotypes. The genome-wide patterns and hotspot regions of ROH provide valuable insights into genetic diversity, demographic history, and selection trends. In this study, we analyzed whole-genome resequencing data from 117 rabbits to identify ROH patterns and inbreeding level across eleven rabbit breeds, including seven Chinese indigenous breeds and four exotic breeds, and to uncover selective signatures based on ROH islands.

RESULTS

We detected a total of 31,429 ROHs across the autosomes of all breeds, with the number of ROHs (NROH) per breed ranging from 1316 to 7476. The mean sum of ROHs length (SROH) per individual was 493.84 Mb, covering approximately 22.79% of the rabbit autosomal genome. The majority of the detected ROHs ranged from 1 to 2 Mb in length, with an average ROH length (LROH) of 1.84 Mb. ROHs longer than 6 Mb constituted only 0.83% of the detected ROHs. The average inbreeding coefficient derived from ROHs (FROH) was 0.23, with FROH values ranging from 0.14 to 0.38 across breeds. Among Chinese indigenous breeds, the Jiuyishan rabbit exhibited the highest values of NROH, SROH, LROH, and FROH, whereas the Fujian Yellow rabbit had the lowest FROH values. In exotic rabbit breeds, the Japanese White rabbit displayed the highest values for NROH, SROH, LROH, and FROH, while the Flemish Giant rabbit had the lowest values for these metrics. Additionally, we identified 17 ROH islands in Chinese indigenous breeds and 22 ROH islands in exotic rabbit breeds, encompassing 124 and 186 genes, respectively. In Chinese indigenous breeds, we identified prominent genes associated with reproduction, including CFAP206, RNF133, CPNE4, ASTE1, and ATP2C1, as well as genes related to adaptation, namely CADPS2, FEZF1, and EPHA7. In contrast, the exotic breeds exhibited a prevalence of genes associated with fat deposition, such as ELOVL3 and NPM3, as well as growth and body weight related genes, including FAM184B, NSMCE2, and TWNK.

CONCLUSIONS

This study enhances our understanding of genetic diversity and selection pressures in domestic rabbits, offering valuable implications for breeding management and conservation strategies.

Genetic diversity and demographic history of the largest remaining migratory population of brindled wildebeest (Connochaetes taurinus taurinus) in southern Africa

The blue wildebeest (Connochaetes taurinus) is a keystone species in the savannahs of southern Africa, where it maintains shortgrass plains and serves as an important prey source for large carnivores. Despite being the second-largest migratory wildebeest population, the brindled wildebeest (C. t. taurinus) of the Greater Liuwa Ecosystem (GLE) of western Zambia have remained largely unstudied, until recently. While studies have increased understanding of recent demography, migration, and population limiting factors, the level of genetic diversity, patterns of gene flow, and long-term demographic history of brindled wildebeest in the GLE remains unknown. Most genetic studies of wildebeest have focused on small, heavily-managed populations, rather than large, migratory populations of high conservation significance. We used restriction-site associated DNA sequencing (RAD-seq) to assess genetic diversity, population structure, and demographic history of brindled wildebeest in the GLE. Using SNPs from 1,730 loci genotyped across 75 individuals, we found moderate levels of genetic diversity in GLE brindled wildebeest (He =  0.210), very low levels of inbreeding (FIS =  0.033), and an effective population size of about one tenth the estimated population size. No genetic population structure was evident within the GLE. Analyses of the site frequency spectrum found signatures of expansion during the Middle Pleistocene followed by population decline in the Late Pleistocene and early Holocene, a pattern previously observed in other African ungulates. These results will supplement field studies in developing effective conservation plans for wildebeest as they face continued and increasing threats of habitat loss, poaching, and other human impacts across their remaining range.

Towards Genetically Informed Conservation of the Bardoka and Karakachan Sheep Breeds Autochthonous to Serbia

Bardoka and Karakachan sheep are primitive regional transboundary Pramenka-type sheep autochthonous to the Balkan Peninsula, whose populations have been reduced to a critically small size in Serbia. We genotyped 105 Bardoka animals (97 ewes and 8 rams from three flocks) and 97 Karakachan sheep (86 ewes and 11 rams from four flocks), along with 28 Ile-de-France (IDF) animals used for a comparison (25 ewes and 3 rams), using 14 nuclear microsatellites to assess their genetic status and establish a foundation for their genetically informed conservation. We utilized genetic data to assess inbreeding values of individuals (I) and pairwise relatedness (r) traditionally inferred from the pedigree data, which are incomplete in the studied autochthonous breeds. We used these data to assemble a data set of unrelated individuals for subsequent genetic analyses. Low but statistically significant genetic differentiation of Bardoka and Karakachan sheep (FST = 0.031, p < 0.01) demonstrates that these phenotypically distinct breeds differ at the genetic level as well. The I and r in ewes were higher in the Karakachan sheep (I = 0.09, r = 0.07) than in Bardoka (I = 0.06, r = 0.06). Contrary to the IDF rams, Bardoka and Karakachan sheep rams were genetically heterogeneous and those of the latter breed displayed higher average r values (0.01 vs. 0.08, respectively). Rams of both local breeds had identical I values of 0.02. Although Bardoka and Karakachan sheep still harbor rather high levels of genetic diversity (HE = 0.761 ± 0.028 and 0.761 ± 0.021, respectively), the overall genetic data demonstrate that the genetic consequences of the population decline were more severe in the latter breed. A genetic structure presenting a general trend of differentiation of flocks with low genetic exchange into separate genetic entities was observed, indicating the effects of genetic drift. The implementation of the genetically informed conservation, together with the ongoing efforts of the state to enlarge the Bardoka and Karakachan sheep populations, would increase the prospects for the long-term survival of both breeds in Serbia.

Integrating in situ strategies and molecular genetics for the conservation of the endangered Azorean endemic plant Lotus azoricus

In this paper, we integrate in situ conservation strategies with population genetic analyses to improve future prospects for preserving the endangered species Lotus azoricus P.W.Ball (Fabaceae), currently found on three islands of the Azores: Santa Maria, Pico, and São Jorge. The two largest populations are in Ponta do Castelo (Santa Maria) and Calheta de Nesquim (Pico). Project LIFE VIDALIA recently implemented a comprehensive conservation plan, which included seed propagation, population reinforcement for four populations on Pico and São Jorge, and control of invasive plant species and rats. To assess genetic diversity and population structure, we analysed L. azoricus populations using retrotransposons. An increase in population size was observed at Calheta de Nesquim following the implementation of these actions, despite the negative impact of Hurricane Lorenzo in 2019. Genetic analysis revealed some admixture, with translocated plants used in reinforcements on Pico showing a distinct founder effect and differing genetic patterns compared to original individuals. Overall genetic differentiation was low, however Saint Lourenço population (Santa Maria) presented significant genetic differentiation. Gene flow between populations was high, likely due to natural or human-mediated seed dispersal. The highest genetic diversity was found at Calheta de Nesquim, likely influenced by gene flow and population growth. Some populations are prioritised for conservation based on high allelic richness and unique genetic markers. To prevent potential loss of genetic diversity, translocation between genetically distinct populations should be avoided. Collaboration between conservation stakeholders and researchers is essential for creating holistic conservation plans, and prior knowledge of population genetics will enable more effective planning.

Karyotype evolution and speciation in Orthoptera

Karyotype evolution might fuel speciation and can thereby contribute to species diversity. To test the hypothesis that speciation and karyotype change are linked, we estimated anagenetic and cladogenetic rates of karyotype evolution as well as speciation rates in Orthoptera. We compiled the male diploid chromosome number and the number of visible chromosome arms (the fundamental number) from published sources for 1,541 species. Chromosome-associated speciation rates were estimated by jointly modelling cladogenetic and anagenetic character evolution and the phylogenetic birth-death process in a Bayesian statistical framework using a subset of 516 species from 14 families. Our findings unveiled heterogeneity among orthopteran families in the pace of karyotype evolution and whether it was linked to speciation. In 6/14 clades, we found evidence supporting speciation-associated (cladogenetic) karyotype changes, while in 6/14 clades karyotype evolution was primarily anagenetic. The remaining clades (2/14) showed uncertainty in favour of either model. We further analyzed whether flightless phenotype, and thus less mobile species, showed higher rates of karyotype evolution. We showed that the flightless phenotype is associated with the rate of chromosome loss. The finding indicates contrasting patterns of karyotype evolution within specific orthopteran lineages, thus emphasizing substantial diversity in the pace of this evolutionary process. It also implies that substantial changes in chromosome number, arising from instances of chromosomal gains and losses, are recurring events in orthopterans that are associated with reproductive isolation and speciation, at least in some groups.

Ancestral process for infectious disease outbreaks with superspreading

When an infectious disease outbreak is of a relatively small size, describing the ancestry of a sample of infected individuals is difficult because most ancestral models assume large population sizes. Given a set of infected individuals, we show that it is possible to express exactly the probability that they have the same infector, either inclusively (so that other individuals may have the same infector too) or exclusively (so that they may not). To compute these probabilities requires knowledge of the offspring distribution, which determines how many infections each infected individual causes. We consider transmission both without and with superspreading, in the form of a Poisson and a Negative-Binomial offspring distribution, respectively. We show how our results can be incorporated into a new Lambda-coalescent model which allows multiple lineages to coalesce together. We call this new model the Omega-coalescent, we compare it with previously proposed alternatives, and advocate its use in future studies of infectious disease outbreaks.

Persistent Habitat Instability and Patchiness, Sexual Attraction, Founder Events, Drift and Selection: A Recipe for Rapid Diversification of Orchids

Orchidaceae is one of the most species-rich families of flowering plants, with most current diversity having evolved within the last 5 My. Patterns associated with species richness and rapid diversification have been identified but have not often been associated with evolutionary processes. We review the most frequently identified correlates of diversity and suggest that the processes and rate by which they occur vary geographically and are largely dependent on persistent pulses of habitat instabilities, especially for epiphytes. Aggressive orogenesis creates fragmented habitats while global climatic cycles exacerbate the ecological instabilities. The need for repeated cycles of dispersal results in frequent founder events, which sets the stage for allopatric diversification via bouts of genetic drift and natural selection. The allopatry requirement can be bypassed by pollination systems involving flowers attracting pollinators through the production of sex signaling semiochemicals. The drift-selection model of diversification, coupled with persistent habitat instability throughout ecological and geological time scales, and sex signaling are the likely components of a multifactorial process leading to the rapid, recent diversification in this family.

Development and Application of Novel SSR Markers to Assess the Genetic Diversity and Population Structure of Phacelia secunda Along an Altitudinal Gradient in the Central Chile Andes

Phacelia secunda J.F. Gmel. (Boraginaceae) is a widely distributed insect-pollinated perennial herb. In central Chile (33° S), it occurs from the sea level up to 3600 m in the Andes, exhibiting broad morphological variation. In this study, we developed and characterized novel polymorphic microsatellites for this species, using an Illimina MiSeq sequencing platform. Nineteen polymorphic loci were obtained, with alleles numbers ranging from 3 to 13 per locus (mean = 5.84). Observed (HO) and expected heterozygosities (HE) ranged from 0.050 to 0.900 and from 0.049 to 0.825, respectively. These markers were applied to assess the genetic diversity and population structure along an altitudinal spanning from 1600 to 3600 m. The highest elevation population exhibited significantly lower within-population genetic diversity compared to lower-elevation populations. Significant population differentiation was observed along the gradient. Gene flow estimates support a stepping-stone like mode of migration, with greater exchange between adjacent elevations. These new microsatellites provide a valuable tool for elucidating the influence of altitude on genetic diversity and structure, and for evaluating the roles of local adaptation and phenotypic plasticity in shaping population variation.

Temporal Variability in Effective Size ( N ̂ e ) Identifies Potential Sources of Discrepancies Between Mark Recapture and Close Kin Mark Recapture Estimates of Population Abundance

Although efforts to estimate effective population size, census size and their ratio in wild populations are expanding, few empirical studies investigate interannual changes in these parameters. Hence, we do not know how repeatable or representative many estimates may be. Answering this question requires studies of long-term population dynamics. Here we took advantage of a rich dataset of seven brook trout (Salvelinus fontinalis) populations, 5 consecutive years and 5400 individuals genotyped at 33 microsatellites to examine variation in estimates of effective and census size and in their ratio. We first estimated the annual effective number of breeders (N ̂ b) using individuals aged 1+. We then adjusted these estimates using two life history traits, to obtainN ̂ b adj 2 and subsequently,N ̂ e adj 2 following Waples et al. (2013).N ̂ e adj 2 was estimated for the years 2014 to 2019. Census size was estimated by mark recapture using double-pass electrofishing (N ̂ c MR ) (years 2014-2018) as well as by the Close Kin Mark Recapture approach (N ̂ c CKMR ) (years 2015-2017). Within populations, annual variation inN ̂ e adj 2 (ratio of maximum to minimumN ̂ e adj 2 ) ranged from 1.6-fold to 58-fold. Over all 7 populations, the median annual variation inN ̂ e adj 2 was around 5-fold. These results reflect important interannual changes in the variance in reproductive success and more generally in population dynamics. Within populationN ̂ c MR varied between years by a (median) factor of 2.7 with a range from 2 to 4.3. Thus, estimated effective size varied nearly twice as much as did estimated census size. Our results therefore suggest that, at least in small populations like those examined in the present study, any single annual estimate ofN ̂ e adj 2 is unlikely to be representative of long-term dynamics. At least 3-4 annual estimates may be required for an estimate of contemporary effective size to be truly representative. We then comparedN ̂ c MR toN ̂ c CKMR . For five of the seven populations, the estimates of population abundance based on mark recapture (N ̂ c MR ) were indistinguishable from those based on close kin mark recapture (N ̂ c CKMR ). The two populations with discordantN ̂ c MR andN ̂ c CKMR exhibited extremely lowN ̂ e adj 2 / N ̂ c MR ratios and the largest annual variation inN ̂ e adj 2 (58-fold and 35.4-fold respectively). These results suggest that sampling effort in these two streams may have been insufficient to properly capture the genetic diversity of the entire population and that individuals sampled were not representative of the population. Our study further validates CKMR as a method for estimating abundance in wild populations and it demonstrates how knowledge of the temporal variation inN ̂ e can be used to identify potential sources of discrepancies betweenN ̂ c MR andN ̂ c CKMR .

Spatial structure facilitates evolutionary rescue by drug resistance

Bacterial populations often have complex spatial structures, which can impact their evolution. Here, we study how spatial structure affects the evolution of antibiotic resistance in a bacterial population. We consider a minimal model of spatially structured populations where all demes (i.e., subpopulations) are identical and connected to each other by identical migration rates. We show that spatial structure can facilitate the survival of a bacterial population to antibiotic treatment, starting from a sensitive inoculum. Specifically, the bacterial population can be rescued if antibiotic resistant mutants appear and are present when drug is added, and spatial structure can impact the fate of these mutants and the probability that they are present. Indeed, the probability of fixation of neutral or deleterious mutations providing drug resistance is increased in smaller populations. This promotes local fixation of resistant mutants in the structured population, which facilitates evolutionary rescue by drug resistance in the rare mutation regime. Once the population is rescued by resistance, migrations allow resistant mutants to spread in all demes. Our main result that spatial structure facilitates evolutionary rescue by antibiotic resistance extends to more complex spatial structures, and to the case where there are resistant mutants in the inoculum.

Assessing the 'Small Population' Paradigm: The Effects of Stochasticity on Evolutionary Change and Population Growth in a Bird Metapopulation

Habitat loss is leading to smaller fragmented populations, increasing their susceptibility to stochasticity. Quantifying the effects of demographic and environmental stochasticity on population dynamics and the contribution of selection versus drift to phenotypic change is essential to assess the potential consequences of environmental change. We examined how stochasticity influenced population growth and body mass changes over 22 years in 11 insular house sparrow (Passer domesticus) populations. Environmental stochasticity induced synchrony in growth rates across populations while also causing substantial island-specific fluctuations. Additionally, demographic stochasticity led to larger annual growth rate fluctuations in smaller populations. Although heavier individuals generally had higher fitness, we detected non-directional evolutionary change in body mass, driven by drift rather than selection. Our study provides a unique quantitative assessment of the 'small population' paradigm, highlighting the importance of theoretically driven analyses of long-term individual-based data to understand the drivers of phenotypic evolution and a population's long-term viability.

Game changing mutation

We present a model of the effect of mutation on haploid sexually reproducing populations by modelling the reproductive dynamics as occurring in the context of a common interests game played by the loci, with the alleles in the role of pure actions. Absent mutations, the population will deterministically converge to a pure Nash equilibrium of the game. A novel mutation adds new alleles, hence is tantamount to a change of the game by the addition of new actions. If the new game defined by the mutation removes the former pure Nash equilibrium the game changing mutation becomes in addition a Nash equilibrium changing mutation, as the population will then move to a new equilibrium with an increase in fitness. A graph of common interests games is defined, and evolution by mutation is modelled as a path through this graph. We discuss two applications-fitness valley crossing and evolutionary contingency.

Bayesian Inference of Pathogen Phylogeography using the Structured Coalescent Model

Over the past decade, pathogen genome sequencing has become well established as a powerful approach to study infectious disease epidemiology. In particular, when multiple genomes are available from several geographical locations, comparing them is informative about the relative size of the local pathogen populations as well as past migration rates and events between locations. The structured coalescent model has a long history of being used as the underlying process for such phylogeographic analysis. However, the computational cost of using this model does not scale well to the large number of genomes frequently analysed in pathogen genomic epidemiology studies. Several approximations of the structured coalescent model have been proposed, but their effects are difficult to predict. Here we show how the exact structured coalescent model can be used to analyse a precomputed dated phylogeny, in order to perform Bayesian inference on the past migration history, the effective population sizes in each location, and the directed migration rates from any location to another. We describe an efficient reversible jump Markov Chain Monte Carlo scheme which is implemented in a new R package StructCoalescent. We use simulations to demonstrate the scalability and correctness of our method and to compare it with existing software. We also applied our new method to several state-of-the-art datasets on the population structure of real pathogens to showcase the relevance of our method to current data scales and research questions.

Multidisciplinary monitoring and stakeholder engagement support large carnivore restoration in human-dominated landscape

Translocations are central to large carnivore restoration efforts, but inadequate monitoring often inhibits effective conservation decision-making. Extinctions, reintroductions, illegal killings, and high inbreeding levels of the Central European populations of Eurasian lynx (Lynx lynx) typify the carnivore conservation challenges in the Anthropocene. Recently, several conservation efforts were initiated to improve the genetic and demographic status but were met with variable success. Here, we report on successful, stakeholder-engaged translocation efforts across three countries aimed to: (1) reinforce the Dinaric lynx population that was suffering from high inbreeding levels and (2) create a new stepping-stone subpopulation in the neighboring Southeastern Alps to help connect the Dinaric and Alpine populations. To evaluate the success of these efforts, we used multidisciplinary and internationally coordinated monitoring using systematic camera trapping, non-invasive genetic sampling, GPS tracking, recording of reproductive events and interspecific interactions, as well as the simultaneous tracking of the public and stakeholders' support of lynx conservation before, during, and after the translocations. Among the 22 translocated wild-caught Carpathian lynx, 68% successfully integrated into the population and local ecosystems, and at least 59% reproduced. The probability of dispersing from the release areas was three times lower with the soft-release method than with hard-release method. Translocated individuals had substantially lower natural mortality and higher reproductive success, while their ecological impact was similar compared to the lynx from the remnant population. Cooperation with local hunters and protected area managers enabled us to conduct multi-year camera-trapping and non-invasive genetic monitoring across a 12,000-km2 transboundary area. Results indicate a reversal in population decline, as the lynx abundance increased for >40% during the 4-year translocation period. Effective inbreeding decreased from 0.32 to 0.08-0.19, suggesting a twofold to fourfold increase in fitness. Furthermore, the successful establishment of a new stepping-stone subpopulation represents an important step toward restoring the Central European lynx metapopulation. Robust partnerships with local communities and hunters, coupled with transparent communication, helped maintain high public and stakeholder support for lynx conservation throughout the translocation efforts. Lessons learned about the importance of stakeholder involvement and multidisciplinary monitoring conducted across several countries provide a successful example for further efforts to restore large carnivores in human-dominated ecosystems.

Isolating selective from non-selective forces using site frequency ratios

A new method is introduced for estimating the distribution of mutation fitness effects using site frequency spectra. Unlike previous methods, which make assumptions about non-selective factors, or that try to incorporate such factors into the underlying model, this new method mostly avoids non-selective effects by working with the ratios of counts of selected sites to neutral sites. An expression for the likelihood of a set of selected/neutral ratios is found by treating the ratio of two Poisson random variables as the ratio of two gaussian random variables. This approach also avoids the need to estimate the relative mutation rates of selected and neutral sites. Simulations over a wide range of demographic models, with linked selection effects show that the new SFRatios method performs well for statistical tests of selection, and it performs well for estimating the distribution of selection effects. Performance was better with weak selection models and for expansion and structured demographic models than for bottleneck models. Applications to two populations of Drosophila melanogaster reveal clear but very weak selection on synonymous sites. For nonsynonymous sites, selection was found to be consistent with previous estimates and stronger for an African population than for one from North Carolina.

Allele ages provide limited information about the strength of negative selection

For many problems in population genetics, it is useful to characterize the distribution of fitness effects (DFE) of de novo mutations among a certain class of sites. A DFE is typically estimated by fitting an observed site frequency spectrum (SFS) to an expected SFS given a hypothesized distribution of selection coefficients and demographic history. The development of tools to infer gene trees from haplotype alignments, along with ancient DNA resources, provides us with additional information about the frequency trajectories of segregating mutations. Here, we ask how useful this additional information is for learning about the DFE, using the joint distribution on allele frequency and age to summarize information about the trajectory. To this end, we introduce an accurate and efficient numerical method for computing the density on the age of a segregating variant found at a given sample frequency, given the strength of selection and an arbitrarily complex population size history. We then use this framework to show that the unconditional age distribution of negatively selected alleles is very closely approximated by reweighting the neutral age distribution in terms of the negatively selected SFS, suggesting that allele ages provide little information about the DFE beyond that already contained in the present day frequency. To confirm this prediction, we extended the standard Poisson random field method to incorporate the joint distribution of frequency and age in estimating selection coefficients, and test its performance using simulations. We find that when the full SFS is observed and the true allele ages are known, including ages in the estimation provides only small increases in the accuracy of estimated selection coefficients. However, if only sites with frequencies above a certain threshold are observed, then the true ages can provide substantial information about the selection coefficients, especially when the selection coefficient is large. When ages are estimated from haplotype data using state-of-the-art tools, uncertainty about the age abrogates most of the additional information in the fully observed SFS case, while the neutral prior assumed in these tools when estimating ages induces a downward bias in the case of the thresholded SFS.

Genetic Diversity and Relationship Among Algerian, Nigerian, and Turkish Goat Breeds Using Microsatellite Markers

BACKGROUND

This study was conducted to identify genetic diversity among goat breeds in Algeria, Türkiye, and Nigeria, which is believed to have arisen due to historical influences, trade networks, and environmental adaptations, using 12 microsatellite markers. Additionally, the study provided insights into the population structure and kinship relationships among the breeds.

METHODS

The animal material of the study consisted of 514 goats from eight breeds: four Algerian (n = 224), two Turkish (n = 140), and two Nigerian (n = 150) native goat breeds. The quality and quantity control of DNA obtained from blood samples was determined using the Nanodrop 2000 device. In the study, 12 microsatellite markers were used. Capillary electrophoresis was used to separate polymerase chain reaction (PCR) fragments labeled with fluorescent dye in the Beckman Coulter GeXP Genetic Analyzer. Statistical analyses were used to calculate molecular genetic parameters, F-statistics, and genetic distances. Factorial correspondence analysis, structure analysis, and dendrogram construction were used to explore population structure.

RESULTS

The study used microsatellite markers to analyze genetic diversity in various breeds, revealing 149 alleles with a mean of 12.41 per locus. Positive inbreeding coefficient within subpopulations (FIS) values indicated a heterozygote deficiency, suggesting potential breeding strategies. Population structure analyses revealed distinct genetic clusters and relationships, providing insights into genetic variation within populations.

CONCLUSION

The study provides a detailed analysis of goat populations in Algeria, Türkiye, and Nigeria, revealing the presence of heterozygote deficiency and the need for strategic breeding interventions to preserve genetic diversity. The findings also reveal distinct genetic clusters and relationships with historical influences, particularly the role of the Mediterranean Sea, adding depth to our understanding. The research offers practical guidance for the sustainable management of these valuable genetic resources, emphasizing adaptive strategies to ensure the resilience and adaptability of goat populations. The findings are crucial for informed decision-making in conserving and utilizing diverse livestock breeds, urging further exploration of goat populations' genetic landscapes.

Study on the characteristics of genetic diversity and population structure of a rare and endangered species of Rhododendron nymphaeoides (Ericaceae) based on microsatellite markers

BACKGROUND

Rhododendron nymphaeoides is explicitly listed as an endangered species in the "the International Union for Conservation of Nature's Red List (IUCN)", "The Red List of Rhododendrons", "Red List of China's Higher Plants" and "Threatened Species List of China's Higher Plants". It is also listed as a provincial-level key protected wild plant in Sichuan, with few individuals in the wild and significant conservation value. The genetic diversity and population structure have never been described, making it difficult to plan conservation strategies for this plant.

RESULTS

This study utilized 15 pairs of microsatellite markers to examine the genetic diversity of 79 samples of R. nymphaeoides sourced from five different geographic populations. A total of 214 alleles were detected, with the average effective number of alleles (Ne) of 7.0324. The averages for the polymorphism information index (PIC) and expected heterozygosity (He) were 0.7832 and 0.8102, respectively, indicating that the R. nymphaeoides populations harbor a rich genetic information content, the genetic differentiation coefficients (FST) average was 1.2607. There was high genetic diversity among populations, with average observed heterozygosity (Ho) and expected heterozygosity (He) values of 0.6375 and 0.6663, respectively, suggesting a degree of inbreeding within populations. Mantel test results showed a significant positive correlation between geographic distance and genetic distance amongst populations (r = 0.8456, P = 0.0021), which conforms to the isolation-by-distance (IBD) model. Due to geographical barriers, there is also a high level of genetic differentiation among populations, with an average genetic differentiation coefficient (FST) of 0.2685. Analysis of molecular variance (AMOVA) indicated that the main source of molecular variance exists within populations (73%), rather than between populations (27%). There was higher historical gene flow (average = 1.0850) and lower contemporary gene flow (average = 1.2849), with seed and pollen dispersal being impeded. Under the Two-Phase Model (TPM) assumption, findings are consistent with the mutation-migration model, suggesting that there has been no genetic bottleneck. STRUCTURE analysis, principal coordinate analysis (PCoA), and UPGMA analysis all support the division of the five natural populations into three genetic clusters.

CONCLUSIONS

This is the first comprehensive analysis of the genetic diversity and population structure of the endangered plant R. nymphaeoides using microsatellite markers. The study results indicate that this endangered plant's natural populations maintain a high level of genetic diversity. Due to geographical barriers, there is also a high level of genetic differentiation, with the primary source of genetic variation originating within populations. There is higher historical gene flow and lower contemporary gene flow, with seed and pollen dispersal being obstructed. The five populations can be divided into three evolutionary units, for which corresponding conservation management units should be established. These findings will benefit the conservation and development of the species and provide a theoretical basis for further studies on its evolution and biogeography.

Conservation genetic evaluation of Juniperus communis sensu lato in Slovakia

This study explores the population structure, hybridization, and adaptation of Juniperus communis sensu lato in the context of its current habitat fragmentation, using inter-primer binding site markers and needle morphometry. Three native juniper taxa in Slovakia were analyzed: J. communis ssp. communis, J. communis ssp. nana, and their putative hybrid, J. communis nothovar. intermedia. The results reveal a moderate overall structure (ΦPT = 0.115, p = 0.001), indicating high gene flow within ssp. communis and low gene flow between ssp. communis and ssp. nana. However, after correcting for non-neutral loci, the inter-subspecies differentiation dropped significantly, suggesting adaptive divergence despite substantial gene flow. This conclusion was further supported using admixture regression of needle morphometry and ΦPT-QST comparison. We show that adaptive genetic differentiation may play a more significant role than phenotypic plasticity in these traits, a key consideration in preventing outbreeding depression in conservation management. Importantly, we also provide evidence for intermediate admixture and distinct selection pressures within two populations of nothovar. intermedia (Stolica, Kralova Studna), which may qualify their recognition as evolutionarily significant units (ESUs).

Contact zones reveal restricted introgression despite frequent hybridization across a recent lizard radiation

Introgression-the exchange of genetic material through hybridization-is now recognized as common among animal species. The extent of introgression, however, can vary considerably even when it occurs: for example, introgression can be geographically restricted or so pervasive that populations merge. Such variation highlights the importance of understanding the factors mediating introgression. Here we used genome-wide SNP data to assess hybridization and introgression at 32 contact zones, comprising 21 phylogenetic independent contrasts across a recent lizard radiation (Heteronotia). We then tested the relationship between the extent of introgression (average admixture at contact zones) and genomic divergence across independent contrasts. Early-generation hybrids were detected at contact zones spanning the range of genomic divergence included here. Despite this, we found that introgression is remarkably rare and, when observed, geographically restricted. Only the two most genomically similar population pairs showed introgression beyond 5 km of the contact zone. Introgression dropped precipitously at only modest levels of genomic divergence, beyond which it was absent or extremely low. Our results contrast with the growing number of studies indicating that introgression is prevalent among animals, suggesting that animal groups will vary considerably in their propensity for introgression.

Extreme genetic signatures of local adaptation in a notorious rice pest, Chilo suppressalis

Climatic variation stands as a significant driving force behind genetic differentiation and the evolution of adaptive traits. Chilo (C.) suppressalis, commonly known as the rice stem borer, is a highly destructive pest that crucially harms rice production. The lack of natural population genomics data has hindered a more thorough understanding of its climate adaptation, particularly the genetic basis underlying adaptive traits. To overcome this obstacle, our study employed completely resequenced genomes of 384 individuals to explore the population structure, demographic history, and gene flow of C. suppressalis in China. This study observed that its gene flow occurred asymmetrically, moving from central populations to peripheral populations. Using genome-wide selection scans and genotype-environment association studies, we identified potential loci that may be associated with climatic adaptation. The most robust signal was found to be associated with cold tolerance, linked to a homeobox gene, goosecoid (GSC), whose expression level was significantly different in low and high latitudes. Moreover, downregulating the expression of this gene by RNAi enhances its cold tolerance phenotypes. Our findings have uncovered and delved into the genetic foundation of the ability of C. suppressalis to adapt to its environment. This is essential in ensuring the continued effectiveness and sustainability of novel control techniques.

Long-term studies provide unique insights into evolution

From experimental evolution in the laboratory to sustained measurements of natural selection in the wild, long-term studies have revolutionized our understanding of evolution. By directly investigating evolutionary dynamics in real time, these approaches have provided unparallelled insights into the complex interplay between evolutionary process and pattern. These approaches can reveal oscillations, stochastic fluctuations and systematic trends that unfold over extended periods, expose critical time lags between environmental shifts and population responses, and illuminate how subtle effects may accumulate into significant evolutionary patterns. Long-term studies can also reveal otherwise cryptic trends that unfold over extended periods, and offer the potential for serendipity: observing rare events that spur new evolutionary hypotheses and research directions. Despite the challenges of conducting long-term research, exacerbated by modern funding landscapes favouring short-term projects, the contributions of long-term studies to evolutionary biology are indispensable. This is particularly true in our rapidly changing, human-dominated world, where such studies offer a crucial window into how environmental changes and altered species interactions shape evolutionary trajectories. In this Review article, we showcase the groundbreaking discoveries of long-term evolutionary studies, underscoring their crucial role in advancing our understanding of the complex nature of evolution across multiple systems and timescales.

Impact of stochastic resetting on resource allocation: The case of reallocating geometric Brownian motion

We study the effects of stochastic resetting on the reallocating geometric Brownian motion (RGBM), an established model for resource redistribution relevant to systems such as population dynamics, evolutionary processes, economic activity, and even cosmology. The RGBM model is inherently nonstationary and non-ergodic, leading to complex resource redistribution dynamics. By introducing stochastic resetting, which periodically returns the system to a predetermined state, we examine how this mechanism modifies RGBM behavior. Our analysis uncovers distinct long-term regimes determined by the interplay between the resetting rate, the strength of resource redistribution, and standard geometric Brownian motion parameters: the drift and the noise amplitude. Notably, we identify a critical resetting rate beyond which the self-averaging time becomes effectively infinite. In this regime, the first two moments are stationary, indicating a stabilized distribution of an initially unstable, mean-repulsive process. We demonstrate that optimal resetting can effectively balance growth and redistribution, reducing inequality in the resource distribution. These findings help us understand better the management of resource dynamics in uncertain environments.

Genomic Insights Into Inbreeding and Adaptive Divergence of Trout Populations to Inform Genetic Rescue

Genetic rescue, specifically translocation to facilitate gene flow among populations and reduce the effects of inbreeding, is an increasingly used approach in conservation. However, this approach comes with trade-offs, wherein gene flow may reduce fitness when populations have adaptive differentiation (i.e., outbreeding depression). A better understanding of the interaction between isolation, inbreeding, and adaptive divergence in key traits, such as life history traits, will help to inform genetic rescue efforts. Stream-dwelling salmonids, such as the westslope cutthroat trout (Oncorhynchus lewisi; WCT), are well-suited for examining these trade-offs because they are increasingly isolated by habitat degradation, exhibit substantial variation in life history traits among populations, and include many species of conservation concern. However, few genomic studies have examined the potential trade-offs in inbreeding versus outbreeding depression in salmonids. We used > 150,000 SNPs to examine genomic variation and inbreeding coefficients in 565 individuals across 25 WCT populations that differed in their isolation status and demographic histories. Analyses of runs of homozygosity revealed that several isolated WCT populations had "flatlined" having extremely low genetic variation and high inbreeding coefficients. Additionally, we conducted genome scans to identify potential outlier loci that could explain life history differences among 10 isolated populations. Genome scans identified one candidate genomic region that influenced maximum length and age-1 to age-2 growth. However, the limited number of candidate loci suggests that the life history traits examined may be driven by many genes of small effect or phenotypic plasticity. Although adaptive differentiation should be considered, the high inbreeding coefficients in several populations suggest that genetic rescue may benefit the most genetically depauperate WCT populations.

Mind the lag: understanding genetic extinction debt for conservation

The delay between disturbance events and genetic responses within populations is a common but surprisingly overlooked phenomenon in ecology and evolutionary and conservation genetics. If not accounted for when interpreting genetic data, this time lag problem can lead to erroneous conservation assessments. We (i) identify life-history traits related to longevity and reproductive strategies as the main determinants of time lags, (ii) evaluate potential confounding factors affecting genetic parameters during time lags, and (iii) propose approaches that allow controlling for time lags. Considering the current unprecedented rate of loss of genetic diversity and adaptive potential, we expect our novel interpretive and methodological framework for time lags to stimulate further research and discussion on the most appropriate approaches to analyse genetic diversity for conservation.

Perspectives on mating-system evolution: comparing concepts in plants and animals

The study of mating systems, defined as the distribution of who mates with whom and how often in a sexually reproducing population, forms a core pillar of evolution research due to their effects on many evolutionary phenomena. Historically, the "mating system" has either been used to refer to the rate of self-fertilization or to the formation of mating pairs between individuals of distinct sexes. Consequently, these two types of mating systems have tended to be studied separately rather than jointly. This separation often means that mating systems are not necessarily researched in a coherent manner that might apply to different types of organisms (e.g., plants versus animals, or hermaphrodites versus dioecious species), even if similar mechanisms may drive the evolution of self-fertilization and mating pair formation. Here, we review the evolution of both plant and animal mating systems, highlighting where similar concepts underlie both these fields and also where differing mechanisms are at play. We particularly focus on the effects of inbreeding, but also discuss the influence of spatial dynamics on mating-system evolution. We end with a synthesis of these different ideas and propose ideas for which concepts can be considered together to move towards a more cohesive approach to studying mating-system evolution.

Optimizing breeding strategies for early-maturing white maize through genetic diversity and population structure

Maize production and productivity in sub-Saharan Africa are constrained by various factors. Assessing the genetic diversity of newly developed elite inbred lines can help identify lines with desirable genes and explore genetic relatedness for heterotic breeding. The objectives of this study were to assess the level of genetic diversity, and population structure, and identify appropriate clustering methods for assigning maize inbreds into heterotic groups. Three hundred and seventy-six elite inbreds extracted from three source populations were genotyped using Diversity Array Technology (DArTtag) mid-density platform. Results from 1904 of 3,305 SNP marker obtained revealed average marker polymorphism information content (PIC) of 0.39, observed heterozygosity of 0.02, gene diversity of 0.37, minor allele frequency of 0.29, Shannon and Simpson indices of 6.86 and 949.09, respectively, and allele richness of 787.70. The optimum sub-population was three defined by an admixture-based model and principal component analysis. The average genetic distance was 0.303 varying from 0.03 (TZEI 2772 × TZEI 2761) to 0.372 (TZEI 2273 × TZEI 2832). For appropriate heterotic classification of the 376 elite inbreds, the use of IBS distance matrix and average linkage clustering method provided the highest cophenetic correlation coefficient (0.97). Three heterotic group (HG) were identified using IBS distance and average linkage clustering method with HG 1 have 188 inbreds, HG 2 having 137, and HG 3 having 59 inbreds. The pedigree-based phylogenetic tree showed substantial consistency with the heterotic groups identified. The F-statistics based on the underlying population structure revealed 10% variation among sub-populations and 90% variation within sub-populations with a moderate level of genetic differentiation (0.10). The elite inbred lines showed a high degree of genetic diversity, which could be beneficial for developing new, early-maturing white hybrids to mitigate production constraints in sub-Saharan Africa.

Bridging Wright-Fisher and Moran models

The Wright-Fisher model and the Moran model are both widely used in population genetics. They describe the time evolution of the frequency of an allele in a well-mixed population with fixed size. We propose a simple and tractable model which bridges the Wright-Fisher and the Moran descriptions. We assume that a fixed fraction of the population is updated at each discrete time step. In this model, we determine the fixation probability of a mutant and its average fixation and extinction times, under the diffusion approximation. We further study the associated coalescent process, which converges to Kingman's coalescent, and we calculate effective population sizes. We generalize our model, first by taking into account fluctuating updated fractions or individual lifetimes, and then by incorporating selection on the lifetime as well as on the reproductive fitness.

Negative global-scale association between genetic diversity and speciation rates in mammals

Genetic diversity is critical for species evolution and their adaptability to global changes, while speciation rate is critical for explaining large-scale patterns of species richness. Exploring correlates of variation in genetic diversity and speciation rates across species is a major interest of evolutionary biologists, but these two questions have mostly been investigated independently. Here, we assess the relationship between intra-specific genetic diversity and speciation rate for 1897 mammal species (~one third of the total diversity) covering all mammalian orders. We find a negative association between mitochondrial genetic diversity and speciation rate across mammalian clades globally. This association is not accounted for by differences in the ecological attributes of species. Our findings suggest a systematic link between micro- and macroevolutionary processes that need to be better understood and considered when investigating determinants of either genetic diversity or speciation rates.

The Chicago school of ecology's evolutionary superorganism and the clements-wright connection

"Organicism" often refers to the idea that ecosystems or communities are, or are like, organisms. Often implicit in early twentieth century, it has been theorized by Clements, relying on physiological and developmental concepts. I investigate the fate of this idea in major attempts of a theoretical synthesis of ecology in the first part of the twentieth century. I first consider Bioecology (1939), by Clements and Shelford, which elaborates clementsian organicism as a general framework for plant and animal ecology. Then I investigate the major animal ecology treatise of the Chicago school ecologists C. Allee, T. Park, O. Park, K. Schmidt and A. Emerson, Principles of animal ecology (1949). I show how they shifted organicism from physiology to evolution, synthesizing inspiration from both Clements and Sewall Wright, got their inspiration in evolutionary biology, and built a systematic correspondence between cells, organisms and communities. I claim that the focus on populations allowed them to apply Darwinian insights at the level of communities. Finally I argue that this theoretical synthesis fell apart in the next decade because of the rise of density-dependent accounts of population regulation.

No detectable effect of urbanization on genetic drift or gene flow in specialist herbivorous insects of milkweed

Urbanization is hypothesized to isolate populations and restrict dispersal, leading to reduced genetic diversity and increased genetic differentiation. We tested this hypothesis in specialist herbivorous insects of milkweed, positing that higher dispersal ability would mitigate the negative effects of urbanization on genetic drift and gene flow, and that these effects would vary with city size. In this study, we collected 383 milkweed insects from urban and rural sites in Toronto, Canada, and five surrounding cities. Using ddRADseq, we generated 145,000 SPNs for monarchs, 10,000 SNPs for beetles, 6,000 SNPs for weevils to quantify genetic diversity, demographic history and population genetic structure. Contrary to our hypotheses, our results indicated no effect of urbanization or dispersal ability on diversity or genetic differentiation. Genetic diversity, measured as π, varied between 0.0013 and 0.0044 across species, with no urban vs. rural component, but with monarchs having >2 X higher diversity compared to beetles and weevils. Similarly, genetic differentiation was generally low, FST varying between 0.01 and 0.28, but there are no consistent trends among urban vs. rural samples for any of the three species. However, demographic analyses revealed a consistent decline in effective population size for all three sampled species, beginning around the last glacial maximum and intensifying over the past 1,000 years. Our findings suggest that both urbanization and dispersal ability have not been a major factor in reducing gene flow or increasing genetic drift among milkweed's herbivorous insect populations. Instead, historical events such as climatic change since the last glacial maximum, and large-scale anthropogenic disturbance in general, have had a more pronounced impact on demography. These results highlight the importance of considering the combined effects of natural and anthropogenic long-term historical processes when studying population genetics in the context of urbanization.

Reading Yule in light of the history and present of macroevolution

Yule's 1925 paper introducing the branching model that bears his name was a landmark contribution to the biodiversity sciences. In his paper, Yule developed stochastic models to explain the observed distribution of species across genera and to test hypotheses about the relationship between clade age, diversity and geographic range. Here, we discuss the intellectual context in which Yule produced this work, highlight Yule's key mathematical and conceptual contributions using both his and more modern derivations and critically examine some of the assumptions of his work through a modern lens. We then document the strange trajectory of his work through the history of macroevolutionary thought and discuss how the fundamental challenges he grappled with-such as defining higher taxa, linking microevolutionary population dynamics to macroevolutionary rates, and accounting for inconsistent taxonomic practices-remain with us a century later.This article is part of the theme issue '"A mathematical theory of evolution": phylogenetic models dating back 100 years'.

Population structure and inbreeding in Harnali sheep through pedigree analysis

The present investigation was carried out to study population structure using pedigree records and to estimate the inbreeding coefficient in closed flock of Harnali sheep. The data records consisted whole population with 2404 animals produced over 24 years (1998-2021) and reference population of 466 animals (year 2018 to 2021) were obtained from closed flock of Harnali sheep at Department of Animal Genetics and Breeding, LUVAS, Hisar (India). The pedigree under analysis included a maximum of nine generations, with 452 animals used as founder. The results showed that mean maximum, complete, and equivalent generations were 3.20, 1.51 and 2.17, respectively. The effective population size was estimated as 202.63. Number of founders contributing to reference population and effective number of founders (fe) for reference population were 115 and 21. The mean average relatedness and generation interval in whole and reference population were 1.86 and 2.19%, and 4.49 ± 0.06 and 4.19 ± 0.10 years, respectively. The average inbreeding rate among studied population was 0.46% in whole population and 0.50% in reference population. Estimated average relatedness (AR) suggested limited allele sharing within the population. The results of general linear modeling showed that there was no significant (P > 0.05) association of inbreeding on various growth and reproduction traits in studied animals. The study concludes that to minimize generation intervals and counteract inbreeding within the closed flock of Harnali sheep, it's imperative to utilize pedigree records to select unrelated sires and to commence the selection of breeding stock at an early stage. These actions could be vital for enhancing genetic advancement and preserving genetic diversity within the flock.

Population genomics reveals strong impacts of genetic drift without purging and guides conservation of bull and giant kelp

Kelp forests are declining in many parts of the northeast Pacific.1,2,3,4 In small populations, genetic drift can reduce adaptive variation and increase fixation of recessive deleterious alleles,5,6,7 but natural selection may purge harmful variants.8,9,10 To understand evolutionary dynamics and inform restoration strategies, we investigated genetic structure and the outcomes of genetic drift and purging by sequencing the genomes of 429 bull kelp (Nereocystis luetkeana) and 211 giant kelp (Macrocystis sp.) from the coastlines of British Columbia and Washington. We identified 6 to 7 geographically and genetically distinct clusters in each species. Low effective population size was associated with low genetic diversity and high inbreeding coefficients (including increased selfing rates), with extreme variation in these genetic health indices among bull kelp populations but more moderate variation in giant kelp. We found no evidence that natural selection is purging putative recessive deleterious alleles in either species. Instead, genetic drift has fixed many such alleles in small populations of bull kelp, leading us to predict (1) reduced within-population inbreeding depression in small populations, which may be associated with an observed shift toward increased selfing rate, and (2) hybrid vigor in crosses between small populations. Our genomic findings imply several strategies for optimal sourcing and crossing of populations for restoration and aquaculture, but these require experimental validation. Overall, our work reveals strong genetic structure and suggests that conservation strategies should consider the multiple health risks faced by small populations whose evolutionary dynamics are dominated by genetic drift.

Global meta-analysis shows action is needed to halt genetic diversity loss

Mitigating loss of genetic diversity is a major global biodiversity challenge1-4. To meet recent international commitments to maintain genetic diversity within species5,6, we need to understand relationships between threats, conservation management and genetic diversity change. Here we conduct a global analysis of genetic diversity change via meta-analysis of all available temporal measures of genetic diversity from more than three decades of research. We show that within-population genetic diversity is being lost over timescales likely to have been impacted by human activities, and that some conservation actions may mitigate this loss. Our dataset includes 628 species (animals, plants, fungi and chromists) across all terrestrial and most marine realms on Earth. Threats impacted two-thirds of the populations that we analysed, and less than half of the populations analysed received conservation management. Genetic diversity loss occurs globally and is a realistic prediction for many species, especially birds and mammals, in the face of threats such as land use change, disease, abiotic natural phenomena and harvesting or harassment. Conservation strategies designed to improve environmental conditions, increase population growth rates and introduce new individuals (for example, restoring connectivity or performing translocations) may maintain or even increase genetic diversity. Our findings underscore the urgent need for active, genetically informed conservation interventions to halt genetic diversity loss.

Low Genetic Diversity and Complex Population Structure in Black Piranha (Serrasalmus rhombeus), a Key Amazonian Predator

The black piranha (Serrasalmus rhombeus), a widely spread species in the rivers of the Amazon basin, plays a vital role as both key predator and important prey. Despite its essential contribution to ecosystem stability, there is a lack of information regarding its genetic diversity and population dynamics in the central Amazon region. As the Amazon continues to undergo environmental changes in the context of growing anthropogenic threats, such knowledge is fundamental for assist in the conservation of this species. This study is the first to analyze the genetic diversity and population structure of S. rhombeus in the central Amazon region using high-resolution genomic data. We employed a Genotyping-by-Sequencing approach with 248 samples across 14 study sites from various tributaries, encompassing diverse water types (black, white, and clear water) and characterized by 34 physiochemical parameters. The data reveals low diversity accompanied by pronounced signs of inbreeding in half of the sites and robust genetic differentiation and variation among sites and within-sites. Surprisingly, we also found evidence of higher dispersal capacity than previously recognized. Our analysis exposed a complex and high population structure with genetic groups exclusive to some sites. Gene flow was low and some groups presented ambiguous genealogical divergence index (gdi) signals, suggesting the occurrence of potential cryptic species. Moreover, our results suggest that the population structure of black piranha appears more influenced by historical events than contemporary factors. These results underscore the need to give greater attention to this keystone species, for which no regulatory framework or conservation strategies is presently in effect.

Comparative population genomics of manta rays has global implications for management

Understanding population connectivity and genetic diversity is of fundamental importance to conservation. However, in globally threatened marine megafauna, challenges remain due to their elusive nature and wide-ranging distributions. As overexploitation continues to threaten biodiversity across the globe, such knowledge gaps compromise both the suitability and effectiveness of management actions. Here, we use a comparative framework to investigate genetic differentiation and diversity of manta rays, one of the most iconic yet vulnerable groups of elasmobranchs on the planet. Despite their recent divergence, we show how oceanic manta rays (Mobula birostris) display significantly higher heterozygosity than reef manta rays (Mobula alfredi) and that M. birostris populations display higher connectivity worldwide. Through inferring modes of colonization, we reveal how both contemporary and historical forces have likely influenced these patterns, with important implications for population management. Our findings highlight the potential for fisheries to disrupt population dynamics at both local and global scales and therefore have direct relevance for international conservation of marine species.