Robert E. Ricklefs’s research while affiliated with University of Missouri–St. Louis and other places

Strong gene flow from outcrossing relatives tends to blur species boundaries, while divergent ecological selection can counteract gene flow. To better understand how these two forces affect the maintenance of species boundaries, we focused on a species complex including a rare species, maple-leaf oak (Quercus acerifolia), which is found in only four disjunct ridges in Arkansas. Its limited range and geographic proximity to co-occurring close relatives create the possibility for genetic swamping. In this study, we gathered genome-wide SNPs using restriction-site associated DNA sequencing (RADseq) from 190 samples of Q. acerifolia and three of its close relatives, Q. shumardii, Q. buckleyi, and Q. rubra. We found that Q. shumardii and Q. acerifolia are reciprocally monophyletic with low support, suggesting incomplete lineage sorting, introgression between Q. shumardii and Q. acerifolia, or both. Analyses that model allele distributions demonstrate that admixture contributes strongly to this pattern. Populations of Q. acerifolia experience gene flow from Q. shumardii and Q. rubra, but we found evidence that divergent selection is likely maintaining species boundaries: 1) ex situ collections of Q. acerifolia have a higher proportion of hybrids compared to the mature trees of the wild populations, suggesting ecological selection against hybrids at the seed/seedling stage; 2) ecological traits co-vary with genomic composition; and 3) Q. acerifolia shows genetic differentiation at loci hypothesized to influence tolerance of radiation, drought, and high temperature. Our findings strongly suggest that in maple-leaf oak, selection results in higher divergence at regions of the genome despite gene flow from close relatives.

We investigated whether celebrated cases of evolutionary radiations of passerine birds on islands have produced exceptional morphological diversity relative to comparable-aged radiations globally. Based on eight external measurements, we calculated the disparity in size and shape within clades, each of which was classified as being tropical or temperate and as having diversified in a continental or an island/archipelagic setting. We found that the distribution of disparity among all clades does not differ substantively from a normal distribution, which would be consistent with a common underlying process of morphological diversification that is largely independent of latitude and occurrence on islands. Disparity is slightly greater in island clades than in those from continents or clades consisting of island and noninsular taxa, revealing a small, but significant, effect of island occurrence on evolutionary divergence. Nonetheless, the number of highly disparate clades overall is no greater than expected from a normal distribution, calling into question the need to invoke key innovations, ecological opportunity, or other factors as stimuli for adaptive radiations in passerine birds.

Aim The increasing spread of vector‐borne diseases has resulted in severe health concerns for humans, domestic animals and wildlife, with changes in land use and the introduction of invasive species being among the main possible causes for this increase. We explored several ecological drivers potentially affecting the local prevalence and richness of avian malaria parasite lineages in native and introduced house sparrows ( Passer domesticus ) populations. Location Global. Time period 2002–2019. Major taxa studied Avian Plasmodium parasites in house sparrows. Methods We analysed data from 2,220 samples from 69 localities across all continents, except Antarctica. The influence of environment (urbanization index and human density), geography (altitude, latitude, hemisphere) and time (bird breeding season and years since introduction) were analysed using generalized additive mixed models (GAMMs) and random forests. Results Overall, 670 sparrows (30.2%) were infected with 22 Plasmodium lineages. In native populations, parasite prevalence was positively related to urbanization index, with the highest prevalence values in areas with intermediate urbanization levels. Likewise, in introduced populations, prevalence was positively associated with urbanization index; however, higher infection occurred in areas with either extreme high or low levels of urbanization. In introduced populations, the number of parasite lineages increased with altitude and with the years elapsed since the establishment of sparrows in a new locality. Here, after a decline in the number of parasite lineages in the first 30 years, an increase from 40 years onwards was detected. Main conclusions Urbanization was related to parasite prevalence in both native and introduced bird populations. In invaded areas, altitude and time since bird introduction were related to the number of Plasmodium lineages found to be infecting sparrows.

Ecological and evolutionary processes underlying spatial variation in signals involved in mate recognition and reproductive isolation are crucial to understanding the causes of population divergence and speciation. Here, to test hypotheses concerning the causes of song divergence, we examine how songs of two sister species of Atlantic Forest suboscine birds with innate songs, the Pyriglena fire-eye antbirds, vary across their ranges. Specifically, we evaluated the influence of isolation by distance and introgressive hybridization, as well as morphological and environmental variation, on geographic variation in male songs. Analyses based on 496 male vocalizations from 63 locations across a 2,200-km latitudinal transect revealed clinal changes in the structure of songs and showed that introgressive hybridization increases both the variability and the homogenization of songs in the contact zone between the two species. We also found that isolation by distance, morphological constraints, the environment, and genetic introgression independently predicted song variation across geographic space. Our study shows the importance of an integrative approach that investigates the roles of distinct ecological and evolutionary processes that influence acoustic signal evolution.

Species delimitation is challenging in lineages that exhibit both high plasticity and introgression. This challenge can be compounded by collection biases, which may downweight specimens morphologically intermediate between traditional species. Additionally, mismatch between named species and observable phenotypes can compromise species conservation. We studied the species boundaries of Quercus acerifolia, a tree endemic to Arkansas, U.S. We performed morphometric analyses of leaves and acorns from 527 field and 138 herbarium samples of Q. acerifolia and its close relatives, Q. shumardii and Q. rubra. We employed two novel approaches: sampling ex situ collections to detect phenotypic plasticity caused by environmental variation and comparing random field samples with historical herbarium samples to identify collection biases that might undermine species delimitation. To provide genetic evidence, we also performed molecular analyses on genome‐wide SNPs. Quercus acerifolia shows distinctive morphological, ecological, and genomic characteristics, rejecting the hypothesis that Q. acerifolia is a phenotypic variant of Q. shumardii. We found mismatches between traditional taxonomy and phenotypic clusters. We detected underrepresentation of morphological intermediates in herbarium collections, which may bias species discovery and recognition. Rare species conservation requires considering and addressing taxonomic problems related to phenotypic plasticity, mismatch between taxonomy and morphological clusters, and collection biases.

Infection by lineages of avian malaria parasites (Apicomplexa: Haemosporida) varies geographically, and some lineages exhibit disjunct distributions. These patterns might be related to differential resistance among host populations reflecting intrinsic characteristics of both the host and the pathogen. In hematophagous parasites in particular, the structure of host hemoglobin can influence parasite development and reproduction. Though variation in avian hemoglobin has been documented across altitudinal gradients, little is known about hemoglobin variation as it relates to infection by the parasites causing avian malaria. We sequenced the αA-globin subunit of the Bananaquit (Coereba flaveola), and related sequence variation to avian malaria infection frequency and parasite lineage identity. We found no association between αA-globin haplotype and infection by particular parasite lineages among all locations, nor any protective association between globin haplotype frequency and the proportion of individuals infected within populations. Phylogeographic structure and genetic variation at the αA-globin locus, including a highly variable intron, is largely concordant with the mitochondrial cytochrome b locus for these same populations, supporting this marker as an independent and variable target with potential application in biogeographic analyses. Keywords alpha-globin, avian malaria, Bananaquit, Coereba flaveola, West Indies Resumen La variación de la globina alfa no predice la infección por malaria aviar en Coereba flaveola • La infección por linajes de parásitos de la malaria aviar (Apicomplexa: Haemosporida) varía geográficamente y algunos linajes exhiben distribuciones discontinuas. Estos patrones podrían estar relacionados con la resistencia diferencial entre las poblaciones de huéspedes, y reflejan las características intrínsecas tanto del huésped como del patógeno. En los parásitos hematófagos, en particular, la estructura de la hemoglobina del huésped puede influir en el desarrollo y la reproducción del parásito. Aunque se ha documentado la variación de la hemoglobina aviar a través de gradientes altitudinales, se sabe poco sobre su variación en relación con la infección por los parásitos que causan la malaria aviar. Secuenciamos la subunidad de globina αA de Coereba flaveola y relacionamos la variación de la secuencia con la frecuencia de infección por malaria aviar y la identidad del linaje del parásito. No encontramos ninguna asociación entre el haplotipo de globina αA y la infección por determinados linajes de parásitos entre localidades; ni ninguna asociación protectora entre la frecuencia del haplotipo de globina y la proporción de individuos infectados dentro de las poblaciones. La estructura filogeográfica y la variación genética en el locus de la globina αA, que incluye un intrón muy variable, concuerdan en gran medida con el locus del citocromo b mitocondrial para estas mismas poblaciones; lo que respalda a este marcador como un objetivo independiente y variable con aplicación potencial en análisis biogeográficos. Palabras clave Caribe Insular, Coereba flaveola, globina alfa, malaria aviar Résumé La variation de l’alpha-globine ne permet pas de prédire l’infection par le paludisme aviaire chez le Sucrier à ventre jaune (Coereba flaveola) • L’infection par des lignées de parasites responsables du paludisme aviaire (Apicomplexa: Haemosporida) varie géographiquement, et certaines lignées présentent des répartitions disjointes. Ces schémas pourraient être liés à une résistance différentielle entre les populations d’hôtes reflétant des caractéristiques intrinsèques à la fois de l’hôte et du pathogène. Dans le cas particulier des parasites hématophages, la structure de l’hémoglobine de l’hôte peut influer sur le développe- ment et la reproduction du parasite. Bien que la variation de l’hémoglobine aviaire ait été documentée en fonction des gradients altitudinaux, peu de choses sont connues sur la variation de l’hémoglobine en relation avec l’infection par les parasites responsables du paludisme aviaire. Nous avons séquencé la sous-unité αA-globine du Sucrier à ventre jaune (Coereba flaveola), et nous avons mis en relation la variation de la séquence avec la fréquence d’infection du paludisme aviaire et l’identité de la lignée parasitaire. Nous n’avons trouvé aucune association entre l’haplotype αA-globine et l’infection par des lignées parasitaires particulières en fonction des sites, ni aucune association protectrice entre la fréquence de l’haplotype globine et la proportion d’individus infectés au sein des populations. La structure phylogéographique et la variation génétique au locus de l’αA-globine, y compris un intron hautement variable, est largement concordante avec le locus du cytochrome b mitochondrial pour ces mêmes populations, indiquant ce marqueur comme une cible indépendante et variable pouvant avoir une application potentielle dans les analyses biogéographiques. Mots clés alpha-globine, Antilles, Coereba flaveola, paludisme aviaire, Sucrier à ventre jaune

Habitat divergence among close relatives is a common phenomenon. Studying the mechanisms behind habitat divergence is fundamental to understanding niche partitioning, species diversification, and other evolutionary processes. Recent studies found that soil microbes regulate the abundance and diversity of plant species. However, it remains unclear whether soil microbes can affect the habitat distributions of plants and drive habitat divergence. To fill in this knowledge gap, we investigated whether soil microbes might restrict habitat distributions of closely related oaks (Quercus spp.) in eastern North America. We performed a soil inoculum experiment using two pairs of sister species (i.e., the most closely related species) that show habitat divergence: Quercus alba (local species) vs. Q. michauxii (foreign), and Q. shumardii (local) vs. Q. acerifolia (foreign). To test whether host‐specific soil microbes are responsible for habitat restriction, we investigated the impact of local sister live soil (containing soil microbes associated with local sister species) on the survival and growth of local and foreign species. Second, to test whether habitat‐specific soil microbes are responsible for habitat restriction, we examined the effect of local habitat live soil (containing soil microbes within local sister's habitats, but not directly associated with local sister species) on the seedlings of local and foreign species. We found that local sister live soil decreased the survival and biomass of foreign species' seedlings while increasing those of local species, suggesting that host‐specific soil microbes could potentially mediate habitat exclusion. In contrast, local habitat live soil did not differentially affect the survival or biomass of the local vs. foreign species. Our study indicates that soil microbes associated with one sister species can suppress the recruitment of the other host species, contributing to the habitat partitioning of close relatives. Considering the complex interactions with soil microbes is essential for understanding the habitat distributions of closely related plants. Why is a species only found in a certain habitat but not in others? Why do closely related species show divergence in habitat preference? Our findings show that host‐specific soil microbes, not habitat‐specific soil microbes, contribute to habitat restriction and partitioning among closely related species.

Birds are highly visually oriented and use plumage coloration as an important signalling trait in social communication. Hence, males and females may have different patterns of plumage coloration, a phenomenon known as sexual dichromatism. Because males tend to have more complex plumages, sexual dichromatism is usually attributed to female choice. However, plumage coloration is partly condition-dependent; therefore, other selective pressures affecting individuals' success may also drive the evolution of this trait. Here, we used tanagers as model organisms to study the relationships between dichromatism and plumage coloration complexity in tanagers with parasitism by haemosporidians, investment in reproduction and life-history traits. We screened blood samples from 2849 individual birds belonging to 52 tanager species to detect haemosporidian parasites. We used publicly available data for plumage coloration, bird phylogeny and life-history traits to run phylogenetic generalized least-square models of plumage dichromatism and complexity in male and female tanagers. We found that plumage dichromatism was more pronounced in bird species with a higher prevalence of haemosporidian parasites. Lastly, high plumage coloration complexity in female tanagers was associated with a longer incubation period. Our results indicate an association between haemosporidian parasites and plumage coloration suggesting that parasites impact mechanisms of sexual selection, increasing differences between the sexes, and social (non-sexual) selection, driving females to develop more complex coloration.

Aim The biotic interactions hypothesis predicts that interactions between species are stronger at lower elevations compared to higher elevations. We tested whether this prediction is met by examining elevational patterns in avian haemosporidian infections in New Guinean birds. Location YUS Conservation Area, Papua New Guinea. Taxon Birds and haemosporidia. Methods We collected blood samples from 2268 individuals of 66 bird species along a reef‐to‐ridgetop tropical elevational gradient covering ~3000 m of elevation. We used molecular methods to screen samples for haemosporidian parasites, and sequenced 70% of positive infections to determine the identity of parasite genera. We fit a phylogenetic generalized mixed‐effects model to test whether infection prevalence was higher at low elevations, as predicted by the biotic interactions hypothesis. Finally, we tested for phylogenetic signal in parasite prevalence and in host elevational distribution using Pagel's λ . Results Overall parasite prevalence was 45% . Infection prevalence decreased with elevation, though prevalence remained above ~30% even for high‐elevation communities between 2000 and 3000 m. We found strong phylogenetic signal in infection prevalence, but no phylogenetic signal in host elevational distribution. Nearly all sequenced infections (97%) were of Haemoproteus. Main Conclusions Our results are consistent with predictions arising from the biotic interactions hypothesis. However, phylogenetic relationships among hosts are a much better predictor of infection prevalence than is elevational position: closely related bird species tend to have similar infection prevalence regardless of the elevations where they live.

Closely related species vary greatly in range size. To understand what drives range‐size variation, we established an integrative framework focusing on two causal pathways: the amount of currently suitable habitat (ASH) and range filling (i.e., the occupancy of ASH). Instead of testing different hypotheses in isolation, we linked four hypotheses to this unifying framework: we tested the niche breadth and niche position hypotheses, which explain range‐size variation via effects on ASH; we also tested the colonization ability and post‐glacial migration lag hypotheses, which explain range‐size variation via range filling. The Americas. Last Glacial Maximum (LGM) to present. One hundred and eighty‐three oak species. We extracted locality records and measured range size as the area of occupancy (AOO) and extent of occurrence (EOO). We used Maxent models and current environmental layers to quantify ASH, niche breadth and niche position. We used seven phenotypic traits as proxies of colonization ability. We calculated post‐glacial accessibility to currently suitable habitat, in addition to the proportion of currently suitable habitat covered by LGM ice sheets. Using structural equation models and regression models, we tested the four hypotheses. Finally, we examined how ASH and range filling contributed interactively to range‐size variation by quantifying variance and covariance. Our results supported all four hypotheses. Additionally, we found that variance in ASH and range filling contributed to a similar extent to variance in AOO, with almost zero covariance between ASH and range filling. In contrast, range filling accounted for almost all the variance in EOO, and we detected a significant negative covariance between ASH and range filling. In oaks, factors associated with range filling are at least as important as niche properties in determining range size. Our framework is generalizable to other study systems for testing the contributions of two pathways, ASH and range filling, to range‐size variation.