Changes in parrot diversity after human arrival to the Caribbean

Zooarchaeology of Managed, Captive, Tame, and Domestic Birds: Shifts in Human-Avian Relationships

In this paper, I review archaeological evidence for shifting human-avian interactions. Many species of birds, altering their behavior in response to anthropogenic niche construction, experienced an increased encounter rate with humans. Intensification of this relationship led to management and domestication of some taxa. An examination of the methods zooarchaeologists employ to study this changing interaction illustrates the limitations of evidence. Art history, architecture, historical sources, evidence based on modern distributions, and DNA analysis fill in some gaps in our knowledge. It is necessary to develop novel methods to investigate the earlier history of bird-human interactions. We also need to consider other taxa behaviorally amenable to domestication, as there was probably a diverse array of past human-bird relationships that remain unknown. Archaeologically, the relationship between people and birds is fundamental to understanding many symbolic and economic practices central to human societies. This review highlights the varied relationships between humans and birds globally allowing cross-regional examination.

Genomic data reveal that the Cuban blue-headed quail-dove (Starnoenas cyanocephala) is a biogeographic relict

Islands are well known for their unique biodiversity and significance in evolutionary and ecological studies. Nevertheless, the extinction of island species accounts for most human-caused extinctions in recent time scales, which have accelerated in recent centuries. Pigeons and doves (Columbidae) are noteworthy for the high number of island endemics, as well as for the risks those species have faced since human arrival. On Caribbean islands, no other columbid has generated more phylogenetic interest and uncertainty than the blue-headed quail-dove, Starnoenas cyanocephala. This endangered Cuban endemic has been considered more similar, both behaviourally and phenotypically, to Australasian species than to the geographically closer 'quail-dove' (Geotrygon s.l.) species of the Western Hemisphere. Here, we use whole genome sequencing from Starnoenas and other newly sequenced columbids in combination with sequence data from previous publications to investigate its relationships. Phylogenomic analyses, which represent 35 of the 51 genera currently comprising the Columbidae, reveal that the blue-headed quail-dove is the sole representative of a lineage diverging early in the radiation of columbids. Starnoenas is sister to the species-rich subfamily Columbinae, which is found worldwide. As a highly distinctive evolutionary lineage lacking close modern relatives, we recommend elevating the conservation priority of Starnoenas.

A phylogenomic tree of wood-warblers (Aves: Parulidae): Dealing with good, bad, and ugly samples

The New World warblers (Parulidae) are a model group for ecological and evolutionary analyses. However, current phylogenetic relationships across this family are based upon few loci. Here we use ultraconserved elements (UCEs) to estimate a rigorous species-level phylogeny for the family. As is true for many groups, high-quality tissues were unavailable for some taxa. Thus, we explored methods for incorporating sequences derived from historical (toe pad) samples to expand the phylogenetic datasets. We recovered an average of 4,186 UCE loci and mitochondrial bycatch data (supplemented with published mitochondrial data) from 96% of all currently recognized species. We found that the UCE phylogeny built with alignments with less than 70% of gaps and ambiguities recovered the most robust phylogenetic relationships for this family, representing 101 species. Using this phylogeny as a topological backbone and adding ten fair quality "bad" samples effectively generated an overall well supported phylogeny, representing 108 species (∼90% of all species). Based on this tree, we then added in seven poor quality "ugly" samples and six of those were placed within their expected genera. We also explored the phylogenetic positions of the likely extinct Leucopeza semperi and the endangered Catharopeza bishopi where limited data was obtained. Overall, taxonomic placements in our UCE trees largely correspond to previously published studies with the recovery of all currently recognized genera as monophyletic except for Basileuterus which was rendered paraphyletic by B. lachrymosus. Our study provides insights in understanding the phylogenetic relationships of a model Passeriformes family and outlines effective practices for managing sparse genomic data sourced from historical museum specimens. Variable topological arrangements across datasets and analyses reflect the evolutionary complexity of this group and provide future topics for in-depth studies.

Hurricanes threaten species and alter evolutionary trajectories on tropical islands

Hurricanes are natural phenomena, but anthropogenic climate change will cause hurricanes to be stronger and more frequent in the future. It has long been known that hurricanes impact plants and animals, but only recently has the impact on biodiversity been mapped globally, showing that species at risk of extinction due to hurricanes are largely restricted to tropical islands. Tropical islands harbor many plants and animals found nowhere else, many of which are currently threatened, and tropical islands have already suffered a disproportionate number of species extinctions due to human activity and introductions of non-native species. The big question is whether species on tropical islands are adapted to hurricane disturbance and will be able to cope with stronger and more frequent storms, or whether tropical islands will see a wave of hurricane-induced extinctions in the future. Here, we discuss this question and how hurricanes will reshuffle interactions between species - such as those between nectarivorous birds and their flowers - and will alter evolutionary trajectories for coadapted species. Moreover, we discuss the role of life history and other taxa-specific traits, such as diet preferences and dispersal ability, both to survive the direct and indirect impact of hurricanes and to recolonize islands when local populations have been eliminated. We also highlight how topographic complexity and island area may buffer against hurricanes; thus, biodiversity on small and low-lying islands should be more impacted than biodiversity on large and mountainous islands. We end by discussing conservation efforts to diminish the detrimental ecological and evolutionary effects of stronger and more frequent hurricanes on tropical islands.

Enhancing biodiversity: historical ecology and biogeography of the Santa Catalina Island ground squirrel, Otospermophilus beecheyi nesioticus

People have influenced Earth's biodiversity for millennia, including numerous introductions of domestic and wild species to islands. Here, we explore the origins and ecology of the Santa Catalina Island ground squirrel (SCIGS; Otospermophilus beecheyi nesioticus), one of only five endemic terrestrial mammals found on California's Santa Catalina Island. We synthesized all records of archaeological/palaeontological SCIGS, conducted radiocarbon dating and stable isotope analysis of the potentially earliest SCIGS remains and performed genetic analysis of modern SCIGS. Squirrels were not identified in island palaeontological deposits, but at least 12 island archaeological sites contain SCIGS bones, including some that are butchered or burned. All directly dated SCIGS bones are Late Holocene in age and younger than approximately 1290 cal BP. The first mitochondrial genome for modern Otospermophilus beecheyi and 15 modern SCIGS mitogenomes document at least one introduction of squirrels. Stable isotope data indicate variable SCIGS diets and potential subsidies from marine environments to terrestrial plants consumed by some individuals. We cannot rule out a natural overwater dispersal, but the earliest SCIGS remains post-date the earliest evidence for people by several millennia and, along with other lines of evidence, support a human-assisted translocation of squirrels during the Late Holocene. These data illustrate the important role of Indigenous people in shaping and enhancing island biodiversity and ecology around the world.

Assembly, Persistence, and Disassembly Dynamics of Quaternary Caribbean Frugivore Communities

AbstractHow communities assemble and restructure is of critical importance to ecological theory, evolutionary theory, and conservation, but long-term perspectives on the patterns and processes of community assembly are rarely integrated into traditional community ecology, and the utility of communities as an ecological concept has been repeatedly questioned in part because of a lack of temporal perspective. Through a synthesis of paleontological and neontological data, I reconstruct Caribbean frugivore communities over the Quaternary (2.58 million years ago to present). Numerous Caribbean frugivore lineages arise during periods coincident with the global origins of plant-frugivore mutualisms. The persistence of many of these lineages into the Quaternary is indicative of long-term community stability, but an analysis of Quaternary extinctions reveals a nonrandom loss of large-bodied mammalian and reptilian frugivores. Anthropogenic impacts, including human niche construction, underlie the recent reorganization of frugivore communities, setting the stage for continued declines and evolutionary responses in plants that have lost mutualistic partners. These impacts also support ongoing and future introductions of invader complexes: introduced plants and frugivores that further exacerbate native biodiversity loss by interacting more strongly with one another than with native plants or frugivores. This work illustrates the importance of paleontological data and perspectives in conceptualizing ecological communities, which are dynamic and important entities.

Introduced and extinct: neglected archival specimens shed new light on the historical biogeography of an iconic avian species in the Mediterranean

Collection specimens provide valuable and often overlooked biological material that enables addressing relevant, long-unanswered questions in conservation biology, historical biogeography, and other research fields. Here, we use preserved specimens to analyze the historical distribution of the black francolin (Francolinus francolinus, Phasianidae), a case that has recently aroused the interest of archeozoologists and evolutionary biologists. The black francolin currently ranges from the Eastern Mediterranean and the Middle East to the Indian subcontinent, but, at least since the Middle Ages, it also had a circum-Mediterranean distribution. The species could have persisted in Greece and the Maghreb until the 19th century, even though this possibility had been questioned due to the absence of museum specimens and scant literary evidence. Nevertheless, we identified four 200-year-old stuffed black francolins-presumably the only ones still existing-from these areas and sequenced their mitochondrial DNA control region. Based on the comparison with conspecifics (n = 396) spanning the entirety of the historic and current species range, we found that the new samples pertain to previously identified genetic groups from either the Near East or the Indian subcontinent. While disproving the former occurrence of an allegedly native westernmost subspecies, these results point toward the role of the Crown of Aragon in the circum-Mediterranean expansion of the black francolin, including the Maghreb and Greece. Genetic evidence hints at the long-distance transport of these birds along the Silk Road, probably to be traded in the commerce centers of the Eastern Mediterranean.