Mind the gap: genetic distance increases with habitat gap size in Florida scrub jays

Dynamics of reduced genetic diversity in increasingly fragmented populations of Florida Scrub‐Jays , Aphelocoma coerulescens

Understanding the genomic consequences of population decline is important for predicting species' vulnerability to intensifying global change. Empirical information about genomic changes in populations in the early stages of decline, especially for those still experiencing immigration, remains scarce. We used 7834 autosomal SNPs and demographic data for 288 Florida scrub jays (Aphelocoma coerulescens; FSJ) sampled in 2000 and 2008 to compare levels of genetic diversity, inbreeding, relatedness, and lengths of runs of homozygosity (ROH) between two subpopulations within dispersal distance of one another but have experienced contrasting demographic trajectories. At Archbold Biological Station (ABS), the FSJ population has been stable because of consistent habitat protection and management, while at nearby Placid Lakes Estates (PLE), the population declined precipitously due to suburban development. By the onset of our sampling in 2000, birds in PLE were already less heterozygous, more inbred, and on average more related than birds in ABS. No significant changes occurred in heterozygosity or inbreeding across the 8‐year sampling interval, but average relatedness among individuals decreased in PLE, thus by 2008 average relatedness did not differ between sites. PLE harbored a similar proportion of short ROH but a greater proportion of long ROH than ABS, suggesting one continuous population of shared demographic history in the past, which is now experiencing more recent inbreeding. These results broadly uphold the predictions of simple population genetic models based on inferred effective population sizes and rates of immigration. Our study highlights how, in just a few generations, formerly continuous populations can diverge in heterozygosity and levels of inbreeding with severe local population decline despite ongoing gene flow.

Staging to join non-kin groups in a classical cooperative breeder, the Florida scrub-jay

1. Why unrelated members form groups in animal societies remains a pertinent topic in evolutionary biology because benefits for group members often are not obvious. We studied subordinates that disperse to join unrelated social groups in the Florida scrub-jay Aphelocoma coerulescens, a cooperative breeding species mainly composed of kin-based groups. 2. We evaluated potential adaptive benefits of dispersing to become an unrelated helper (staging) versus remaining home and dispersing only to pair and breed (direct dispersal) to understand why non-kin-based groups form. 3. Using 35 years of demographic data, we quantified life history aspects of staging individuals and tested associations between social and ecological factors on the natal and staging territories. We compared fitness outcomes between dispersal strategies by analyzing survival, breeding recruitment, and direct reproductive output. We tested for sexual asymmetry potentially driven by differences in territory acquisition patterns and female-biased dispersal for this species. 4. Of birds that reached one-year-old, 28% staged at a non-natal territory before breeding or disappearing. Staging dispersers departed at younger ages and moved greater distances than direct dispersers. When looking at proximate factors on the natal territory associated with staging, males left groups with many same-sex helpers, while females often left when their father disappeared. For both sexes, staging individuals more likely came from high-quality territories and joined groups with fewer same-sex helpers than in their natal group. While staging and direct dispersers did not differ in survival or likelihood of becoming a breeder, staging males became breeders later and had lower lifetime reproductive success than direct dispersers. 5. In Florida scrub-jays, staging appears to be an alternative strategy for female helpers, but a best-of-a-bad-situation for males. This sexual asymmetry is consistent with males having more options than females to achieve higher reproductive success by breeding near home. Tradeoffs in cost-benefits of departing the natal territory and joining unrelated groups as a helper seem to best explain alternative dispersal patterns, with optimal social queues primarily driving the benefits. This research highlights plasticity in dispersal behavior in response to social and environmental conditions and offers a new perspective in our understanding of non-kin-based social groups.

Spatial structure and dispersal dynamics in a house sparrow metapopulation

The effects of spatial structure on metapopulation dynamics depend upon the interaction between local population dynamics and dispersal, and how this relationship is affected by the geographical isolation and spatial heterogeneity in habitat characteristics. Our aim is to examine how emigration and immigration of house sparrows Passer domesticus in a Norwegian archipelagic metapopulation are affected by key factors predicted by classic metapopulation models to affect dispersal-spatial and temporal variation in population size, inter-island distance, local demography and habitat characteristics. This metapopulation can be divided into two major habitat types: (a) islands closer to the mainland where sparrows breed in colonies on farms, and (b) islands without farms, situated farther away from the mainland where sparrows are exposed to harsher environmental conditions. Dispersal was spatially structured within the metapopulation; there was proportionally and numerically less emigration and immigration involving farm islands, as compared to non-farm islands. Furthermore, emigration and immigration occurred mostly between nearby islands. Moreover, emigration in response to spatial differences in mean population size differed between the habitat types, but populations with large mean received more immigrants in both habitat types. The number of emigrants and immigrants was negatively related to long-term recruit production, which was not the case in non-farm islands. The proportion and number of emigrants was positively related to temporal increases in recruit production on farm islands, however not on non-farm islands. Our results demonstrate that spatial heterogeneity in environmental conditions influences how spatial variation in long-term mean population size, and temporal and spatial variation in recruit production, affects dispersal dynamics. The spatial structure of this metapopulation is therefore best described by a spatially explicit model in which the exchange of individuals within each habitat type is strongly affected by the degree of geographical isolation, population size and recruit production. However, these relationships differed between the two habitat types; non-farm islands showing similarities to a mainland-island model type of structure, whereas farm islands showed features more associated with source-sink or balanced dispersal models. Such differential dispersal dynamics between habitat types are expected to have important consequences for the ecological and evolutionary dynamics within this metapopulation.

Half of resources in threatened species conservation plans are allocated to research and monitoring

Funds to combat biodiversity loss are insufficient, requiring conservation managers to make trade-offs between costs for actions to avoid further loss and costs for research and monitoring to guide effective actions. Using species' management plans for 2328 listed species from three countries we show that 50% of species' proposed recovery plan budgets are allocated to research and monitoring. The proportion of budgets allocated to research and monitoring vary among jurisdictions and taxa, but overall, species with higher proportions of budgets allocated to research and monitoring have poorer recovery outcomes. The proportion allocated to research and monitoring is lower for more recent recovery plans, but for some species, plans have allocated the majority of funds to information gathering for decades. We provide recommendations for careful examination of the value of collecting new information in recovery planning to ensure that conservation programs emphasize action or research and monitoring that directly informs action.

Deconstructing isolation-by-distance: The genomic consequences of limited dispersal

Geographically limited dispersal can shape genetic population structure and result in a correlation between genetic and geographic distance, commonly called isolation-by-distance. Despite the prevalence of isolation-by-distance in nature, to date few studies have empirically demonstrated the processes that generate this pattern, largely because few populations have direct measures of individual dispersal and pedigree information. Intensive, long-term demographic studies and exhaustive genomic surveys in the Florida Scrub-Jay (Aphelocoma coerulescens) provide an excellent opportunity to investigate the influence of dispersal on genetic structure. Here, we used a panel of genome-wide SNPs and extensive pedigree information to explore the role of limited dispersal in shaping patterns of isolation-by-distance in both sexes, and at an exceedingly fine spatial scale (within ~10 km). Isolation-by-distance patterns were stronger in male-male and male-female comparisons than in female-female comparisons, consistent with observed differences in dispersal propensity between the sexes. Using the pedigree, we demonstrated how various genealogical relationships contribute to fine-scale isolation-by-distance. Simulations using field-observed distributions of male and female natal dispersal distances showed good agreement with the distribution of geographic distances between breeding individuals of different pedigree relationship classes. Furthermore, we built coalescent simulations parameterized by the observed dispersal curve, population density, and immigration rate, and showed how incorporating these extensions to Malécot’s theory of isolation-by-distance allows us to accurately reconstruct observed sex-specific isolation-by-distance patterns in autosomal and Z-linked SNPs. Therefore, patterns of fine-scale isolation-by-distance in the Florida Scrub-Jay can be well understood as a result of limited dispersal over contemporary timescales.

Dispersal is a fundamental component of the life history of most organisms and therefore influences many biological processes. Dispersal is particularly important in creating genetic structure on the landscape. We often observe a pattern of decreased genetic relatedness between individuals as geographic distances increases, or isolation-by-distance. This pattern is particularly pronounced in organisms with extremely short dispersal distances. Despite the ubiquity of isolation-by-distance patterns in nature, there are few examples that explicitly demonstrate how limited dispersal influences spatial genetic structure. Here we investigate the processes that result in spatial genetic structure using the Florida Scrub-Jay, a bird with extremely limited dispersal behavior and extensive genome-wide data. We take advantage of the long-term monitoring of a contiguous population of Florida Scrub-Jays, which has resulted in a detailed pedigree and measurements of dispersal for hundreds of individuals. We show how limited dispersal results in close genealogical relatives living closer together geographically, which generates a strong pattern of isolation-by-distance at an extremely small spatial scale (<10 km) in just a few generations. Given the detailed dispersal, pedigree, and genomic data, we can achieve a fairly complete understanding of how dispersal shapes patterns of genetic diversity over short spatial scales.

A population genetic window into the past and future of the walleye Sander vitreus: relation to historic walleye and the extinct "blue pike" S. v. "glaucus"

Background

Conserving genetic diversity and local adaptations are management priorities for wild populations of exploited species, which increasingly are subject to climate change, habitat loss, and pollution. These constitute growing concerns for the walleye Sander vitreus, an ecologically and economically valuable North American temperate fish with large Laurentian Great Lakes' fisheries. This study compares genetic diversity and divergence patterns across its widespread native range using mitochondrial (mt) DNA control region sequences and nine nuclear DNA microsatellite (μsat) loci, examining historic and contemporary influences. We analyze the genetic and morphological characters of a putative endemic variant– “blue pike” S. v. “glaucus” –described from Lakes Erie and Ontario, which became extinct. Walleye with turquoise-colored mucus also are evaluated, since some have questioned whether these are related to the “blue pike”.

Results

Walleye populations are distinguished by considerable genetic divergence (mean F_ST mtDNA = 0.32 ± 0.01, μsat = 0.13 ± 0.00) and substantial diversity across their range (mean heterozygosity mtDNA = 0.53 ± 0.02, μsat = 0.68 ± 0.03). Southern populations markedly differ, possessing unique haplotypes and alleles, especially the Ohio/New River population that houses the oldest haplotype and has the most pronounced divergence. Northern formerly glaciated populations have greatest diversity in Lake Erie (mean heterozygosity mtDNA = 0.79 ± 0.00, μsat = 0.72 ± 0.01). Genetic diversity was much less in the historic Lake Erie samples from 1923–1949 (mean heterozygosity mtDNA = 0.05 ± 0.01, μsat = 0.47 ± 0.06) than today. The historic “blue pike” had no unique haplotypes/alleles and there is no evidence that it comprised a separate taxon from walleye. Turquoise mucus walleye also show no genetic differentiation from other sympatric walleye and no correspondence to the “blue pike”.

Conclusions

Contemporary walleye populations possess high levels of genetic diversity and divergence, despite habitat degradation and exploitation. Genetic and previously published tagging data indicate that natal homing and spawning site philopatry led to population structure. Population patterns were shaped by climate change and drainage connections, with northern ones tracing to post-glacial recolonization. Southerly populations possess unique alleles and may provide an important genetic reservoir. Allelic frequencies of Lake Erie walleye from ~70–90 years ago significantly differed from those today, suggesting population recovery after extensive habitat loss, pollution, and exploitation. The historic “blue pike” is indistinguishable from walleye, indicating that taxonomic designation is not warranted.

Fragmentation of Atlantic forest has not affected gene flow of a widespread seed-dispersing bat

Habitat loss and resultant fragmentation are major threats to biodiversity, particularly in tropical and subtropical ecosystems. It is increasingly urgent to understand fragmentation effects, which are often complex and vary across taxa, time and space. We determined whether recent fragmentation of Atlantic forest is causing population subdivision in a widespread and important Neotropical seed disperser: Artibeus lituratus (Chiroptera: Phyllostomidae). Genetic structure within highly fragmented forest in Paraguay was compared to that in mostly contiguous forest in neighbouring Misiones, Argentina. Further, observed genetic structure across the fragmented landscape was compared with expected levels of structure for similar time spans in realistic simulated landscapes under different degrees of reduction in gene flow. If fragmentation significantly reduced successful dispersal, greater population differentiation and stronger isolation by distance would be expected in the fragmented than in the continuous landscape, and genetic structure in the fragmented landscape should be similar to structure for simulated landscapes where dispersal had been substantially reduced. Instead, little genetic differentiation was observed, and no significant correlation was found between genetic and geographic distance in fragmented or continuous landscapes. Furthermore, comparison of empirical and simulated landscapes indicated empirical results were consistent with regular long-distance dispersal and high migration rates. Our results suggest maintenance of high gene flow for this relatively mobile and generalist species, which could be preventing or significantly delaying reduction in population connectivity in fragmented habitat. Our conclusions apply to A. lituratus in Interior Atlantic Forest, and do not contradict broad evidence that habitat fragmentation is contributing to extinction of populations and species, and poses a threat to biodiversity worldwide.