Fine-scale genetic structure and its consequence in breeding aggregations of a passerine bird

The pattern of fine-scale genetic structure in a population may reflect current biological processes of the species, such as natal dispersal, the breeding system and demography. We investigated the spatial distribution of nests and fine-scale genetic structure during two breeding seasons in a population of a weakly territorial, flock-living passerine bird, the vinous-throated parrotbill, Paradoxornis webbianus . Nest distribution was clustered. There were two peaks of egg laying within each breeding season, and spatial clustering of nests was more extreme during the second peak after controlling for breeding density. The patterns of genetic structure during the breeding season varied with parental sex and season. Genetic structure occurred during the second laying peak: males breeding within 200 m of one another at this time were significantly more closely related than males breeding farther apart. However, no apparent genetic structure was detected in males during the first laying peak or among females in either laying peak. These results reveal male-oriented kin affiliation during part of the breeding season in this species. Furthermore, juvenile recruitment into the winter flocks was positively related to this increased relatedness among males via kin affiliation. This study implies that fine-scale genetic structure during the breeding season could be a factor determining individual fitness and may play an important role in our understanding of the evolution of social systems.     

Microgeographic population structure of green swordail fish: genetic differentiation despite abundant migration

Swordtails (Xiphophorus; Poeciliidae) have figured prominently in research on fish mating behaviours, sexual selection, and carcinogenesis, but their population structures and dispersal patterns have been relatively neglected. Using nine microsatellite loci, we estimated genetic differentiation in Xiphophorus helleri within and between adjacent streams in Belize. The genetic data were complemented by a tagging study of movement within one stream. In the absence of physical dispersal barriers (waterfalls), population structure followed an isolation by distance (IBD) pattern. Genetic differentiation (F_ST up to 0.07) was significant between and within creeks, despite high dispersal in the latter as judged by the tagging data. Such heterogeneity apparently was a result of genetic drift in local demes, due to small population sizes and highly skewed paternity. The IBD pattern was interrupted by waterfalls, boosting F_ST above 0.30 between adjacent samples across these barriers. Overall, our results are helpful in understanding the interplay of evolutionary forces and population dynamics in a small fish living in a changeable habitat.     

Microgeographic genetic structure and intraspecific parasitism in the ant Leptothorax nylanderi

1. Genetic colony structure of the small central European ant Leptothorax nylanderi is affected strongly by ecological constraints such as nest site availability and intraspecific social parasitism. 2. Although L. nylanderi is generally monogynous and monandrous, more than a quarter of all nests collected in a dense population near Würzburg, Germany, contained several matrilines. As shown by microsatellite analysis, the average nest‐mate relatedness in these nests was 0.20. Genetically heterogeneous nests arise from nest take‐over by alien colonies or founding queens, a result of severe competition for nest sites. 3. In summer, more than one‐third of all colonies inhabited several nest sites at a time. Polydomy appears to be rather limited, with two or three nests belonging to a single polydomous colony. 4. Queens appear to dominate male production; only a small fraction (8%) of males was definitively not progeny of the queen present but might have been worker progeny or offspring of another queen. 5. Strong evidence for heterozygote deficiency was found and a total of nine diploid males was discovered in two colonies. These findings suggest deviation from random mating through small, localised nuptial flights.     

Microgeographic population structure of brook charr: a comparison of microsatellite and mark-recapture data

Polymorphism at five microsatellite genetic markers (genotyped n  = 496) and mark-recapture tagging data (tagged n  = 9813) were used to define the population structure of brook charr, Salvelinus fontinalis from the Indian Bay watershed, Newfoundland, Canada. Despite the absence of physical barriers to migration among lakes, both genetic and tagging data suggest that brook charr in each lake represent reproductively isolated populations. Exact tests comparing allele frequencies, θ (global value = 0·063), R st (global value = 0·052), individual assignment tests, and Nei's genetic distance provided congruent estimates of population subdivision in agreement with the tagging data (only 2·2% of recaptures were lake-to-lake). The genetic structure of the brook charr populations corresponded with the geographic structure of the drainage basin on a qualitative level, although linear distance over water was not significantly correlated with the tagging data or the genetic distance measures. The agreement between the tagging and the genetic data suggest that microsatellite markers can be useful tools for defining real biological units. The results also suggest that brook charr exhibit microgeographic population structure at the watershed scale, and that this is the scale at which conservation and management of this salmonid might best be implemented.     

Cryptic speciation in a Holarctic passerine revealed by genetic and bioacoustic analyses

There has been much controversy regarding the timing of speciation events in birds, and regarding the relative roles of natural and sexual selection in promoting speciation. Here, we investigate these issues using winter wrens ( Troglodytes troglodytes ), an unusual example of a passerine with a Holarctic distribution. Geographical variation has led to speculation that the western North American form Troglodytes troglodytes pacificus might be a distinct biological species compared to those in eastern North America (e.g. Troglodytes troglodytes hiemalis ) and Eurasia. We located the first known area in which both forms can be found, often inhabiting neighbouring territories. Each male wren in this area sings either western or eastern song, and the differences in song are as distinct in the contact zone as they are in allopatry. The two singing types differ distinctly in mitochondrial DNA sequences and amplified fragment length polymorpism profiles. These results indicate that the two forms are reproductively isolated to a high degree where they co-occur and are therefore separate species. DNA variation suggests that the initial split between the two species occurred before the Pleistocene, quite long ago for sister species in the boreal forest. Surprisingly, the two forms are similar in morphometric traits and habitat characteristics of territories. These findings suggest that sexual selection played a larger role than habitat divergence in generating reproductive isolation, and raise the possibility that there are other such morphologically cryptic species pairs in North America.     

Ecological and life-history correlates of cooperative breeding in South African birds

Our analyses of the incidence of cooperative breeding among South African birds differ from previous studies performed elsewhere in two respects. First, we distinguish between obligate (i.e. regular) and facultative (i.e. opportunistic) cooperative breeding species (OCS and FCS). Second, we have restricted our analyses to 217 South African bird species considered to be sufficiently well-studied in terms of their basic biology and life-history characteristics. This was done in order to control for the well-known bias against the often poorly-studied avifaunas of extreme environments such as rainforests and deserts. The results of our analysis do not accord fully with those of Australian birds by Ford et al. (1988). Cooperative breeding in South Africa is associated with seasonal environments, whereas in Australia the opposite is the case. Analyses of ecological factors that promote cooperative breeding among South African birds suggest that the evolutionary pathway to obligate and facultative breeding may be fundamentally different. First, OCS live mainly in savanna habitats that have predictable seasonal peaks in food availability, yet where the baseline level of food availability during the nonbreeding season is sufficient to support permanent residence by groups. Small to medium-sized birds of the African savannas are particularly vulnerable to avian predators, and foraging and roosting in permanent groups may enhance their survival. We propose that the benefits of obligate cooperative breeding are derived chiefly from survival of individuals away from the nest (i.e. during the nonbreeding season). Secondly, FCS live largely in unpredictable, seasonal steppe habitats. Under these conditions it may be impossible for birds to maintain permanent group territories, and variation in the tendency to breed cooperatively may depend largely on the opportunistic assessment of environmental conditions. We therefore suggest that birds (i.e. FCS) will opt to breed cooperatively only when conditions are unfavourable for independent breeding, and that the benefits thus accrued are chiefly related to reproduction.     

Microgeographic genetic structure and gene flow in Hibiscus moscheutos (Malvaceae) populations

Microgeographic genetic variation in populations of a wetland macrophyte, Hibiscus moscheutos L. (Malvaceae), was investigated using allozyme polymorphism. The species is a self-compatible insect-pollinated perennial, and seeds are water dispersed (hydrochory). Six hundred plants were analyzed from eight brackish and two freshwater populations within the Rhode River watershed/estuarine system. The genetic structure of the populations was assessed by fixation indices and spatial autocorrelation analyses. The degree of genetic differentiation among sites and gene flow between all paired combinations of sites (M ) was analyzed using three hypothetical gene flow models. Fixation indices indicated almost complete panmixia within populations, and spatial autocorrelations showed that genotypes were randomly distributed within sites, most likely the result of water dispersal of seeds. Allele frequencies were significantly different among sites, and estimated FST indicated moderate genetic differentiation (_ = 0.062). Genetic differences between populations were mostly explained by a gene flow model that accounted for the location of populations relative to the tidal stream. The importance of hydrochory in affecting spatial genetic structure was thus suggested both within and among H. moscheutos populations.     

Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding

Crop populations derived from experimental crosses enable the genetic dissection of complex traits and support modern plant breeding. Among these, multi-parent populations now play a central role. By mixing and recombining the genomes of multiple founders, multi-parent populations combine many commonly sought beneficial properties of genetic mapping populations. For example, they have high power and resolution for mapping quantitative trait loci, high genetic diversity and minimal population structure. Many multi-parent populations have been constructed in crop species, and their inbred germplasm and associated phenotypic and genotypic data serve as enduring resources. Their utility has grown from being a tool for mapping quantitative trait loci to a means of providing germplasm for breeding programmes. Genomics approaches, including de novo genome assemblies and gene annotations for the population founders, have allowed the imputation of rich sequence information into the descendent population, expanding the breadth of research and breeding applications of multi-parent populations. Here, we report recent successes from crop multi-parent populations in crops. We also propose an ideal genotypic, phenotypic and germplasm ‘package’ that multi-parent populations should feature to optimise their use as powerful community resources for crop research, development and breeding.Subject terms: Plant genetics, Plant breeding, Agricultural genetics, Quantitative trait

Over recent years, numerous multi-parent populations (MPPs) have been successfully developed in crops (Huang et al. 2015; Cockram and Mackay 2018). MPPs bring together key genomic, phenotypic and germplasm resources to form a platform for research and development. In this review, we examine three themes covering new developments in crop MPP research: (1) we survey the rapidly expanding variety of crop MPPs, explaining how differences in their design and construction affect their power and precision in mapping quantitative trait loci (QTL), on which we provide a brief primer. (2) We review the use of genomic technologies in MPPs, which have proven particularly suitable for gathering dense genomic information across large populations. We make general recommendations for collecting genotypic resources in MPPs. (3) We discuss successful applications of MPPs, particularly where they have been used for breeding and pre-breeding. This includes the identification of QTL, the application of genomic prediction to MPPs, and the direct use of MPP lines as germplasm for varietal release or pre-breeding. These recent developments have shown the potential of MPPs for crop improvement.     

The building-up of social relationships: behavioural types, social networks and cooperative breeding in a cichlid

Consistent individual differences in behavioural types may not only cause variation in life-history decisions, but may also affect the choice of social partners and sociality in general. Here, we tested whether and how behavioural type influences the establishment of social ties using the cooperatively breeding cichlid, Neolamprologus pulcher. In a habitat saturation experiment with individuals pre-tested for behavioural type, we first analysed whether behavioural type affected the likelihood of settlement (i.e. social status), group sizes, and the types of dominant and subordinate individuals accepted as group members. Corrected for effects of body size and sex, the behavioural type did not affect settlement. However, bold dominant males only accepted smaller females, and grouped with bold subordinates, while shy dominant males accepted larger females than themselves, and grouped with shy subordinates. Second, we analysed the relationships between behavioural type and the aggressiveness or affiliation social network. Behavioural type significantly affected the number and quality of connections within the two networks. We show that behavioural types affect group composition, social networks and status achieved, in interaction with body size. Thus, the interactions within groups may depend not only on age, size and sex, but also on the behavioural type of the individuals involved.     

Towards an e-biology of ageing: integrating theory and data

Ageing is a highly complex process; it involves interactions between numerous biochemical and cellular mechanisms that affect many tissues in an organism. Although work on the biology of ageing is now advancing quickly, this inherent complexity means that information remains highly fragmented. We describe how a new web-based modelling initiative is seeking to integrate data and hypotheses from diverse biological sources.     

Control of invasive predators improves breeding success of an endangered alpine passerine

Birds living in alpine environments are becoming increasingly impacted by human‐induced threats. We investigated the impacts of introduced mammalian predators on an endangered alpine species, the New Zealand Rockwren Xenicus gilviventris, and assessed whether predator control improved its breeding success. Nest monitoring revealed that the primary cause of nest failure was predation by invasive mammals, primarily Stoats Mustela erminea and House Mice Mus musculus. Daily survival rates (DSR) decreased with nest age, and nests were at their most vulnerable to predators just prior to fledging. DSR, egg‐hatching and fledgling rates were all improved by predator trapping, demonstrating the significant impacts that even low numbers of invasive predators can have on sensitive alpine and upland species.     

The evolution of cooperative breeding in the African cichlid fish,Neolamprologus pulcher

The conundrum of why subordinate individuals assist dominants at the expense of their own direct reproduction has received much theoretical and empirical attention over the last 50 years. During this time, birds and mammals have taken centre stage as model vertebrate systems for exploring why helpers help. However, fish have great potential for enhancing our understanding of the generality and adaptiveness of helping behaviour because of the ease with which they can be experimentally manipulated under controlled laboratory and field conditions. In particular, the freshwater African cichlid, Neolamprologus pulcher, has emerged as a promising model species for investigating the evolution of cooperative breeding, with 64 papers published on this species over the past 27 years. Here we clarify current knowledge pertaining to the costs and benefits of helping in N. pulcher by critically assessing the existing empirical evidence. We then provide a comprehensive examination of the evidence pertaining to four key hypotheses for why helpers might help: (1) kin selection; (2) pay‐to‐stay; (3) signals of prestige; and (4) group augmentation. For each hypothesis, we outline the underlying theory, address the appropriateness of N. pulcher as a model species and describe the key predictions and associated empirical tests. For N. pulcher, we demonstrate that the kin selection and group augmentation hypotheses have received partial support. One of the key predictions of the pay‐to‐stay hypothesis has failed to receive any support despite numerous laboratory and field studies; thus as it stands, the evidence for this hypothesis is weak. There have been no empirical investigations addressing the key predictions of the signals of prestige hypothesis. By outlining the key predictions of the various hypotheses, and highlighting how many of these remain to be tested explicitly, our review can be regarded as a roadmap in which potential paths for future empirical research into the evolution of cooperative breeding are proposed. Overall, we clarify what is currently known about cooperative breeding in N. pulcher, address discrepancies among studies, caution against incorrect inferences that have been drawn over the years and suggest promising avenues for future research in fishes and other taxonomic groups.     

Testable predictions from realistic neural network simulations of vestibular compensation: integrating the behavioural and physiological data

Neural network simulations have been used previously in the investigation of the horizontal vestibulo-ocular reflex (HVOR) and vestibular compensation. The simulations involved in the present research were based on known anatomy and physiology of the vestibular pathway. This enabled the straightforward comparison of the network response, both in terms of behavioural (eye movement) and physiological (neural activity) data to empirical data obtained from guinea pig. The network simulations matched the empirical data closely both in terms of the static symptoms (spontaneous nystagmus) of unilateral vestibular deafferentation (UVD) as well as in terms of the dynamic symptoms (decrease in VOR gain). The use of multiple versions of the basic network, trained to simulate individual guinea pigs, highlighted the importance of the particular connections: the vestibular ganglion to the type I medial vestibular nucleus (MVN) cells on the contralesional side. It also indicated the significance of the relative firing rate in type I MVN cells which make excitatory connections with abducens cells as contributors to the variability seen in the level of compensated response following UVD. There was an absence of any difference (both in terms of behavioural and neural response) between labyrinthectomised and neurectomised simulations. The fact that a dynamic VOR gain asymmetry remained following the elimination of the spontaneous nystagmus in the network suggested that the amelioration of both the static and dynamic symptoms of UVD may be mediated by a single network. The networks were trained on high acceleration impulse stimuli but displayed the ability to generalise to low frequency, low acceleration sinusoids and closely approximated the behavioural responses to those stimuli. Received: 12 October 1998 / Accepted in revised form: 11 February 1999     

植物的繁育系统、遗传结构和遗传多样性保护

达尔文和最早的群体遗传学理论,都认为繁育系统对生物的遗传多样性和进化起重要作用。本文首先介绍用蛋白质电泳检测植物繁育系统的优点,然后讨论中外学者的实验结果,表明在植物众多特征中,如生活型、是有性繁殖还是无性繁殖等都能影响群体遗传结构,但最显著的是繁育系统和群体遗传分化两者间的关系。因此我们能从植物的繁育系统推测群体遗传结构,进而提出监测遗传多样性的取样策略,这对就地保护和移地保护都是十分重要的     

Fine-scale genetic structure and dispersal in cooperatively breeding apostlebirds

In cooperatively breeding species, restricted dispersal of offspring leads to clustering of closely related individuals, increasing the potential both for indirect genetic benefits and inbreeding costs. In apostlebirds (Struthidea cinerea), philopatry by both sexes results in the formation of large (up to 17 birds), predominantly sedentary breeding groups that remain stable throughout the year. We examined patterns of relatedness and fine-scale genetic structure within a population of apostlebirds using six polymorphic microsatellite loci. We found evidence of fine-scale genetic structure within the study population that is consistent with behavioural observations of short-distance dispersal, natal philopatry by both sexes and restricted movement of breeding groups between seasons. Global F(ST) values among breeding groups were significantly positive, and the average level of pairwise relatedness was significantly higher for individuals within groups than between groups. For individuals from different breeding groups, geographical distance was negatively correlated with pairwise relatedness and positively correlated with pairwise F(ST). However, when each sex was examined separately, this pattern was significant only among males, suggesting that females may disperse over longer distances. We discuss the potential for kin selection to influence the evolution and maintenance of cooperative breeding in apostlebirds. Our results demonstrate that spatial genetic structural analysis offers a useful alternative to field observations in examining dispersal patterns of cooperative breeders.     

Population genetic structure across dissolved oxygen regimes in an African cichlid fish

Ecological isolation is a process whereby gene flow between selective environments is reduced due to selection against maladapted dispersers, migrant alleles, or hybrids. Although ecological isolation has been documented in several systems, gene flow can often be high among selective regimes, and more studies are thus needed to better understand the conditions under which ecological gradients or divergent selective regimes should influence population structure. We test for ecological isolation in a system in which high plasticity occurs with respect to traits that are adaptive in alternate forms under different environmental conditions. Pseudocrenilabrus multicolor victoriae is a widespread haplochromine cichlid fish in East Africa that exploits both normoxic (normal oxygen) rivers/lakes and hypoxic (low oxygen) swamps. Here, we examine population structure, using mitochondrial DNA and microsatellites, to determine if genetic divergence is significantly increased between dissolved oxygen regimes relative to within them, while controlling for geographical structure. Our results indicate that geographical separation influences population structure, while no effects of divergent selection with respect to oxygen regimes were detected. Specifically, we document (i) genetic clustering according to geographical region, but no clustering according to oxygen regime; (ii) higher genetic variation among than within regions, but no effect of oxygen regime on genetic variation; (iii) isolation by distance within one region; and (iv) decreasing genetic variability with increasing geographical distance from Lake Victoria. We speculate that plasticity may be facilitating gene flow between oxygen regimes in this system.     

Molecular ecology of social behaviour: analyses of breeding systems and genetic structure

Molecular genetic studies of group kin composition and local genetic structure in social organisms are becoming increasingly common. A conceptual and mathematical framework that links attributes of the breeding system to group composition and genetic structure is presented here, and recent empirical studies are reviewed in the context of this framework. Breeding system properties, including the number of breeders in a social group, their genetic relatedness, and skew in their parentage, determine group composition and the distribution of genetic variation within and between social units. This group genetic structure in turn influences the opportunities for conflict and cooperation to evolve within groups and for selection to occur among groups or clusters of groups. Thus, molecular studies of social groups provide the starting point for analyses of the selective forces involved in social evolution, as well as for analyses of other fundamental evolutionary problems related to sex allocation, reproductive skew, life history evolution, and the nature of selection in hierarchically structured populations. The framework presented here provides a standard system for interpreting and integrating genetic and natural history data from social organisms for application to a broad range of evolutionary questions.     

Testing alternative mechanisms of evolutionary divergence in an African rain forest passerine bird

Abstract Models of speciation in African rain forests have stressed either the role of isolation or ecological gradients. Here we contrast patterns of morphological and genetic divergence in parapatric and allopatric populations of the Little Greenbul, Andropadus virens, within different and similar habitats. We sampled 263 individuals from 18 sites and four different habitat types in Upper and Lower Guinea. We show that despite relatively high rates of gene flow among populations, A. virens has undergone significant morphological divergence across the savanna-forest ecotone and mountain-forest boundaries. These data support a central component of the divergence-with-gene-flow model of speciation by suggesting that despite large amounts of gene flow, selection is sufficiently intense to cause morphological divergence. Despite evidence of isolation based on neutral genetic markers, we find little evidence of morphological divergence in fitness-related traits between hypothesized refugial areas. Although genetic evidence suggests populations in Upper and Lower Guinea have been isolated for over 2 million years, morphological divergence appears to be driven more by habitat differences than geographic isolation and suggests that selection in parapatry may be more important than geographic isolation in causing adaptive divergence in morphology.