Genomic signatures of isolation, hybridization, and selection during speciation of island finches

Sister species occurring sympatrically on islands are rare and offer unique opportunities to understand how speciation can proceed in the face of gene flow. The São Tomé grosbeak is a massive-billed, 'giant' finch endemic to the island of São Tomé in the Gulf of Guinea, where it has diverged from its co-occurring sister species the Príncipe seedeater, an average-sized finch that also inhabits two neighbouring islands. Here, we show that the grosbeak carries a large number of unique alleles different from all three Príncipe seedeater populations, but also shares many alleles with the sympatric São Tomé population of the seedeater, a genomic signature signifying divergence in isolation as well as subsequent introgressive hybridization. Furthermore, genomic segments that remain unique to the grosbeak are situated close to genes, including genes that determine bill morphology, suggesting the preservation of adaptive variation through natural selection during divergence with gene flow. This study reveals a complex speciation process whereby genetic drift, introgression, and selection during periods of isolation and secondary contact all have shaped the diverging genomes of these sympatric island endemic finches.

A supergene underlies linked variation in color and morphology in a Holarctic songbird

The genetic architecture of a phenotype can have considerable effects on the evolution of a trait or species. Characterizing genetic architecture provides insight into the complexity of a given phenotype and, potentially, the role of the phenotype in evolutionary processes like speciation. We use genome sequences to investigate the genetic basis of phenotypic variation in redpoll finches (Acanthis spp.). We demonstrate that variation in redpoll phenotype is broadly controlled by a ~55-Mb chromosomal inversion. Within this inversion, we find multiple candidate genes related to melanogenesis, carotenoid coloration, and bill shape, suggesting the inversion acts as a supergene controlling multiple linked traits. A latitudinal gradient in ecotype distribution suggests supergene driven variation in color and bill morphology are likely under environmental selection, maintaining supergene haplotypes as a balanced polymorphism. Our results provide a mechanism for the maintenance of ecotype variation in redpolls despite a genome largely homogenized by gene flow.

Environmental correlates and functional consequences of bill divergence in island song sparrows

Inferring the environmental selection pressures responsible for phenotypic variation is a challenge in adaptation studies as traits often have multiple functions and are shaped by complex selection regimes. We provide experimental evidence that morphology of the multifunctional avian bill is related to climate, not foraging efficiency, in song sparrows (Melospiza melodia) on the California Channel Islands. Our research builds on a study in song sparrow museum specimens that demonstrated a positive correlation between bill surface area and maximum temperature, suggesting a greater demand for dry heat dissipation in hotter, xeric environments. We sampled contemporary sparrow populations across three climatically distinct islands to test the alternate hypotheses that song sparrow bill morphology is either a product of vegetative differences with functional consequences for foraging efficiency or related to maximum temperature and, consequently, important for thermoregulation. Measurements of >500 live individuals indicated a significant, positive relationship between maximum temperature and bill surface area when correcting for body size. In contrast, maximum bite force, seed extraction time, and vegetation on breeding territories (a proxy for food resources) were not significantly associated with bill dimensions. While we cannot exclude the influence of foraging ability and diet on bill morphology, our results are consistent with the hypothesis that variation in song sparrows' need for thermoregulatory capacity across the northern Channel Islands selects for divergence in bill surface area.

Morphology of migration: Associations between wing shape, bill morphology, and migration in kingbirds (Tyrannus)

Morphology is closely linked to locomotion and diet in animals. In animals that undertake long-distance migrations, limb-morphology is under selection to maximize mobility and minimize energy expenditure. Migratory behaviors also interact with diet, such that migratory animals tend to be dietary generalists, while sedentary taxa tend to be dietary specialists. Despite a hypothesized link between migration status and morphology, phylogenetic comparative studies have yielded conflicting findings. In this study, we tested for evolutionary associations between migratory status and limb and bill morphology across kingbirds, a pan-American genus of birds with migratory, partially migratory, and sedentary taxa. We found that migratory kingbirds had longer and more pointed wings, in agreement with expectations if selection favors improved aerodynamics for long-distance migration. We also found an association between migratory status and bill shape, such that more migratory taxa had wider and deeper bills and sedentary taxa had longer bills. However, there was no difference in levels of intraspecific morphological variation among migrants, partial migrants, and residents, suggesting that dietary specialization has evolved independently of migration strategy. Evolutionary links between migration, diet, and morphology in kingbirds further strengthen ecomorphological associations that underlie long-distance seasonal movements in animals.

Homogeneity in cranial biometrics and bill morphology is verified by measurements from The Gambia, Botswana and Kenya in the case of the putative sub-species of the highly commensal Hooded Vulture Necrosyrtes monachus monachus and non-commensal Necrosyrte

We present biometrical data assembled from a combined total of 37 complete and partially cleaned skulls and feathered heads for the two putative subspecies of Hooded Vulture Necrosyrtes monachus monachus and N. m. pileatus (which Mundy et al. (1992) credibly argue should be N. m. carunculatus). We report on mostly insignificant variation in measurements taken from across three regions of the Hooded Vulture range. For N. m. pileatus (n = 22) the measurements are assembled from 13 live birds captured, tagged and released in Botswana between 2014-2017, seven museum specimens held in The National Museums of Kenya collected during 1913-1950, and two as described below. We compare with N. m. monachus (n = 14) where we measured eight specimens produced by road traffic accidents in The Gambia 2002-2019 of which seven are cleaned bare skulls and one a feathered study skin. We also measured six feathered heads and three skulls from several different countries in Africa, collected during 1832-1929 (n = 6 monachus, 2 pileatus, and 1 unknown) and held at the Natural History Museum, Tring, UK. Cranial materials for Hooded Vulture are scarce in world museums and the Gambian sample consisting of seven cleaned skulls represents the largest known number for a single country. Different populations across the regions vary considerably in both feeding habits and home ranges. We hypothesised that different foraging ecologies may have led to adaptation in bill morphology. Presented here for the first time are a series of skull morphometrics which test for variation in cranial biometrics and bill morphology from across the range of the Hooded Vulture. The Gambian bird has been DNA sequenced and a planned genetics study of other populations will resolve the long-standing taxonomic debate.

Avian diet and foraging ecology constrain foreign egg recognition and rejection

Egg rejection is a common and effective defense against avian brood parasitism in which the host either marginalizes or removes the parasitic egg or deserts the parasitized clutch. The ability to recognize and reject a parasitic egg depends on bill morphology, sensory systems, and cognition, all of which are also shaped by other selective processes such as foraging. This begs the question whether specific phenotypes associated with different foraging strategies and diets may constrain or facilitate egg recognition and rejection. Here, we propose a novel hypothesis that host species phenotypes related to foraging ecology and diet may impose morphological and visual sensory constraints on the evolution of egg recognition and rejection. We conducted a comparative analysis of the adult diets and egg rejection rates of 165 current host and non-host species. We found that species have significantly higher egg rejection rates when they (1) consume an omnivorous or animal and fruit dominated diet rather than seeds and grains, (2) forage arboreally rather than aerially or on the ground, or (3) possess relatively larger body sizes. Although correlational in nature, as predicted, these results suggest phenotypes related to specific diets and foraging ecologies may differentially constrain or facilitate evolution of host egg rejection defenses against avian brood parasitism.

Context-dependent effects of relative temperature extremes on bill morphology in a songbird

Species increasingly face environmental extremes. Morphological responses to changes in average environmental conditions are well documented, but responses to environmental extremes remain poorly understood. We used museum specimens to investigate relationships between a thermoregulatory morphological trait, bird bill surface area (SA) and a measure of short-term relative temperature extremity (RTE), which quantifies the degree that temperature maxima or minima diverge from the 5-year norm. Using a widespread, generalist species, Junco hyemalis , we found that SA exhibited different patterns of association with RTE depending on the overall temperature regime and on precipitation. While thermoregulatory function predicts larger SA at higher RTE, we found this only when the RTE existed in an environmental context that opposed it: atypically cold minimum temperature in a warm climate, or atypically warm maximum temperature in a cool climate. When environmental context amplified the RTE, we found a negative relationship between SA and RTE. We also found that the strength of associations between SA and RTE increased with precipitation. Our results suggest that trait responses to environmental variation may qualitatively differ depending on the overall environmental context, and that environmental change that extremifies already-extreme environments may produce responses that cannot be predicted from observations in less-extreme contexts.

Bill disparity and feeding strategies among fossil and modern penguins

One of the most remarkable differences between Paleogene penguins and their living relatives is the shape and length of their beaks. Many of the Eocene and Oligocene penguins have a thin and elongated spear-like bill, which contrasts with the proportionally shorter and more robust bill of most living species. These differences suggest an important shift in their feeding strategies. This study explores the morphological disparity on the skull of penguins, emphasizing bill morphology and it relationship with feeding habits. For this, the skulls of 118 species of aquatic birds, including 21 fossil and living penguins, were analyzed using two-dimensional geometric morphometric. The results show that, unlike what has been reported for modern birds overall, in penguins and Aequornithes, bill elongation is related to a reduction of the braincase. The discriminant analysis shows that there are significant differences between penguins that feed near or far from the coast and between those that consume nectonic and planktonic prey, identifying Madrynornis as the only extinct form with a possibly planktonic diet. Additionally, it is clear that Paleogene penguins occupy a region of morphospace unexplored by most diving birds, with the western grebe being their closest modern analogue. This is consistent with the hypothesis that giant penguins hunted by harpooning and not by biting as living forms do, signaling a significant change in the habits of those birds leading to the emergence of their crown group.