No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
Cryptic differentiation in the Manx Shearwater hinders the identification of a new endemic subspecies
Journal of Avian Biology
Abstract
The taxonomy of Procellariiformes, particularly petrels and shearwaters, is still unresolved. The Manx shearwater Puffinus puffinus is one of the best studied seabirds worldwide. Most of the information known on this seabird is focused on the northern core populations where the species is abundant. However, the species shows a high number of peripheral populations, which are extremely small and difficult to study in comparison to central populations. Using an integrative approach, we provided significant evidence of phenological, morphological, acoustic, plumage colour, and genetic differentiation of the Canarian Manx shearwaters (the most southern population) from the northern breeding colonies, which is compatible with a long period of isolation. Birds from the Canary Islands breed around 2‐3 months earlier, are smaller and lighter, and show darker underwing plumage than those from northern populations. In addition, Canarian call features are different from the northern populations. Finally, genetic analyses of the mitochondrial control region indicate an incipient genetic differentiation of Canarian Manx shearwaters from the other breeding populations. The Canarian population holds a small number of breeding colonies and it is declining, so accurate taxonomic recognition critically affects conservation efforts. For all the aforementioned reasons, we propose to rank the Canarian breeding population as a new taxon by presenting the formal description of a new subspecies Puffinus puffinus canariensis ssp. nova.
This article is protected by copyright. All rights reserved.
... lherminieri, P. baroli, P. boydi) (Ferrer Obiol et al., 2021). However, the group is still under contentious ongoing taxonomic debate (Sangster et al., 2005;Olson, 2010;Genovart et al., 2012;Ramos et al., 2020;Rodríguez et al., 2020). ...
... Recently, the Canary Islands populations have been described as a new subspecies (P. p. canariensis) based on multiple sources of evidence (Rodríguez et al., 2020). In addition, there is some uncertainty as to the taxonomic affinities of the Madeiran population of P. puffinus (Gil-Velasco et al., 2015;Rodríguez et al., 2020). ...
... p. canariensis) based on multiple sources of evidence (Rodríguez et al., 2020). In addition, there is some uncertainty as to the taxonomic affinities of the Madeiran population of P. puffinus (Gil-Velasco et al., 2015;Rodríguez et al., 2020). ...
Speciation is a continuous and complex process shaped by the interaction of numerous evolutionary forces. Despite the continuous nature of the speciation process, the implementation of conservation policies relies on the delimitation of species and evolutionary significant units (ESUs). Puffinus shearwaters are globally distributed and threatened pelagic seabirds. Due to remarkable morphological status the group has been under intense taxonomic debate for the past three decades. Here, we use double digest Restriction-Site Associated DNA sequencing (ddRAD-Seq) to genotype species and subspecies of North Atlantic and Mediterranean Puffinus shearwaters across their entire geographical range. We assess the phylogenetic relationships and population structure among and within the group, evaluate species boundaries, and characterise the genomic landscape of divergence. We find that current taxonomies are not supported by genomic data and propose a more accurate taxonomy by integrating genomic information with other sources of evidence. Our results show that several taxon pairs are at different stages of a speciation continuum. Our study emphasises the potential of genomic data to resolve taxonomic uncertainties, which can help to focus management actions on relevant taxa, even if they do not necessarily coincide with the taxonomic rank of species.
... The park is home to over 25 breeding bird species, of which three are endemic to Madeira (Regulus madeirensis, Fringilla maderensis, and Columba trocaz), three bat species, and to the endemic Madeira wall lizard (Teira dugesii). Furthermore, the park hosts the only known breeding colony of the Manx shearwater (Puffinus puffinus) in Madeira Island, a regionally threatened seabird, whose population size and ecology in Macaronesia is poorly known (Nunes et al., 2010;Rodríguez et al., 2020). In addition to cats, the list of invasive mammals inhabiting the park include black and Norway rats (Rattus rattus and R. norvegicus, respectively), domestic mice (Mus musculus), European rabbits (Oryctolagus cuniculus) and ferrets (Mustela furo) (Soto et al., 2023(Soto et al., , 2024. ...
... In our study, the absence of seabirds as prey, specifically the Manx shearwater (Puffinus puffinus), can be justified by the fact that sample collection did not occur during the nesting season or the time of fledging of this species (Nunes et al., 2010). This, combined with the reduced estimated population size of this species in Madeira (Rodríguez et al., 2020), might explain their absence in our samples. According to Bonnaud et al. (2011), seabirds can become the preferred prey item of insular cats during their breeding season. ...
Oceanic island ecosystems are particularly vulnerable to the impacts of introduced mammalian predators. Among these, free-ranging cats (Felis catus) are especially detrimental, and have been linked to the extinction and population decline of numerous insular taxa. Yet, a more holistic understanding of the impacts of free-ranging cats has been hampered by an incomplete understanding of their diet and population densities. Using a peri-urban protected area in the subtropical Madeira Island as a case study, we combined DNA metabarcoding, morphological scat analyses, and camera trapping to investigate the magnitude of native and introduced prey consumption by cats. Based on 58 scats collected over the summer and autumn of 2021, we found that cats consume over 20 distinct taxa from ten orders, including native and non-native prey, as well as taxa associated with anthropogenic food. Cat diet was seasonally modulated, with a higher incidence of reptiles in the summer months. Although DNA metabarcoding revealed a higher diversity of prey taxa compared to traditional morphological scat analyses, both methods provided complementary insights, highlighting the benefits of their combined use. Combining our diet results with a free-ranging cat density of 1.4 cats/km², as revealed by the protected area-wide camera trap survey, we estimate an annual prey intake of over 18,000 vertebrates by cats in a protected area of 7.5 km², of which over one-third corresponds to native birds and reptiles. These findings underscore the complex interactions between cats and native wildlife, emphasising the need for targeted conservation strategies in ecologically sensitive areas.
... Macaronesian birds have contributed to improve our understanding of a plethora of ecological and evolutionary topics, for instance, assembly of land bird communities (Triantis et al., 2022), sympatric speciation by allochrony in seabirds (Friesen et al., 2007;Ramos et al., 2016;Rodríguez et al., 2020) and classic island syndromes such as the 'island rule' effect (Benítez-López et al., 2021) and the evolution of flightlessness (Rando et al., 1999;Sayol et al., 2020). Allochrony refers to when populations of a species breed in different temporal windows. ...
... variation in morphological, colour pattern and acoustic traits), but we know that many taxa show similar phenotypes despite having experienced long periods of reproductive isolation (e.g. Kvist et al., 2005;Illera et al., 2018;Rodríguez et al., 2020). This cryptic differentiation could be a consequence of a high degree of niche conservatism without ecological speciation. ...
... Due to their geographic isolation that favors processes such as founder events, selection, and genetic drift among others that lead to phenotypic and genetic differentiation, island species represent a good opportunity to study diversification processes [3,4]. Birds are widely used as models to study diversification processes [e.g., [5][6][7][8][9]. To understand the origin of these variations, different kinds of information can be used [6]. ...
... To understand the origin of these variations, different kinds of information can be used [6]. For example: morphology, particularly bill characteristics [8,10,11], acoustic [12,13], genetic [14,15], phenotypic [16,17], and even more accurately the multicharacter approaches [e.g., 5,6,9]. One mechanism for diversification that can lead to population differentiation and ultimately to speciation, is hybridization [references in 18]. ...
The Setophaga petechia complex includes 43 subspecies distributed within the new world, of which some are migratory and others are resident, with only two resident subspecies in the Mexican Caribbean: Setophaga petechia bryanti a mangrove subspecies belonging to the erithachorides group resident on the mainland of the Yucatan Peninsula and Setophaga petechia rufivertex endemic to Cozumel Island and belonging to the petechia group. Recently, a new population of individuals presenting intermediate phenotypic traits and living in mangrove ecosystems was discovered and reported for Cozumel Island. In this study, we used a multi-character approach including genetic (five ISSR genetic markers), morphometric (eight traits), phenotypic (four characteristics of males), and acoustic dataset (11 parameters) to understand the process of differentiation and the status of these new island individuals in relation to the two well-established subspecies using a total of 60 individuals (20 for each group). Through multivariate analyses based on different dataset used in our study, we show how the new population is related to the endemic island subspecies, S. p. rufivertex and to the mainland subspecies, S. p. bryanti while demonstrating finite differences. We conclude that the new population of S. petechia on Cozumel Island is a well-established population with high level of differentiation.
... Es muy probable, que el patrón migratorio de las aves canarias sea similar al de las aves europeas, aunque con una fenología más adelantada, ya que las primeras aves están presentes en las aguas canarias desde mediados de enero, abandonando los últimos pollos sus nidos a finales de julio (Rodríguez et al., 2020). ...
... parejas reproductoras (Hernández et al., 1990;Medina en Lorenzo, 2007;BirdLife International, 2015), pero la dificultad para acceder a sus colonias y nidos, la escasez de colonias conocidas y sus hábitos de cría (visitas nocturnas y nidificación bajo tierra) hacen muy difícil su estudio. De hecho, en la actualidad no existen datos precisos sobre el tamaño de la población y la mejor evidencia de su reproducción es el hallazgo de pollos deslumbrados por la iluminación de núcleos urbanos (Rodríguez et al., 2008;Rodríguez et al., 2020). ...
... Cryptic speciation refers to the genetic divergence of species with little or no morphological differentiation. This process is widespread in Procellariformes, including albatrosses (Eda et al. 2020, Abeyrama et al. 2021, shearwaters (Rodríguez et al. 2020), and storm petrels ). Due to a lack of clearly discernable morphological differences, most cryptic bird species have been described only recently, aided by the advent of molecular techniques. ...
Divergence in reproductive timing, known as allochrony, is an evolutionary process that in some cases has led to sympatric speciation. However, the mechanisms that could drive the existence of allochrony (e.g., environmental variability), and the role of the ecological adaptations to different seasons in the process of speciation are less known. Further, considering that several allochronic species of birds are threatened, it is important to improve our understanding of their ecology and their management and protection. Our work assessed whether seasonal allochrony has led to phenotypic and ecological differentiation and identified the environmental factors favoring it in Northern storm-petrels (Hydrobatidae).
First, considering that a key aspect in the study of allochrony is a good understanding of the species’ phenology, we assessed breeding phenology using several approaches (e.g. nest monitorin or deployment of geolocators). This included an evaluation of whether brood patch scoring serves as a reliable method for describing phenology in allochronic populations. Second, to understand the role of body size in the seasonal adaptations to the environmental temperature, we assessed whether Bergmann’s rule was met across all allochronic species
and populations of Northern storm-petrels. Third, to assess the role of other ecological adaptations to the environment, we focused on two contrasting systems of allochronic storm petrels, whose genetic differentiation have been well stablished but there is little knowledge on their ecological differentiation. In the first system, comprising the spring-breeding (hot season) and autumn-breeding (cool season) populations of the Cape Verde storm-petrel (Hydrobates jabejabe), which breed in Cabo Verde within the Eastern Tropical Atlantic, minimal genetic differentiation exists between them. In the second system, the summerbreeding
Townsend’s storm-petrel (Hydrobates socorroensis) and the winter- breeding Ainley’s storm-petrel (Hydrobates cheimnomnestes), which breed in Guadalupe Island within the subtropical Mexican Pacific, allochrony has led to a relevant genetic differentiation and they are regarded as sister species. For both systems, we compared the spatial ecology using GPS (for the breeding season) and geolocators (for the non-breeding season), and trophic ecology using isotopes between the allochronic populations. Overall, we found a greater ecological differentiation between populations with a greater genetic differentiation than in those with little differentiation. That is, body size and all the explored axes of the ecological niche were more differentiated between allochronic populations in
Guadalupe than in Cabo Verde. Regarding factors promoting allochrony and differentiation between populations, we found that Guadalupe shows a more pronounced temporal variation in marine productivity and night length compared to Cabo Verde. This implies that differentiation is more likely to occur within highly seasonal systems, encompassing variables such as air temperature, night length and oceanic productivity. These conditions favour reproductive isolation between populations, thereby facilitating differentiation and, ultimately, speciation. In addition, our research revealed that individuals from the allochronic populations of Guadalupe visited previously unrecognized and primarily non-overlaping areas during both, the breeding and the non-breeding periods. This discovery brings new
challenges to the management of the waters between United States and México. Further research is needed in other allochronic organisms, such as mice and fishes, to ascertain whether phenotypic, ecological, physiological and genetic differentiation among allochronic populations co-vary with the intensity of the seasonality and the allochronic speciation process.
... On Ireland's Rathlin Island for instance, ferrets have caused a drastic reduction in the local population of Atlantic puffin (Fratercula arctica) and gulls (Larus spp.), as well as the local extirpation of Manx shearwater (Puffinus puffinus) (Bodey et al. 2011). In addition to Calonectris borealis and Pterodroma madeira, Madeira Island is home to multiple other ground-nesting species of seabirds such as Macaronesian Manx shearwaters (Puffinus puffinus canariensis) and Madeiran storm petrels (Hydrobates castro) (Meirinho et al. 2014;Rodríguez et al. 2020), which are also likely to be affected by ferrets and other non-native mammalian predators. Additionally, ferrets can prey on multiple other species that play crucial roles on Madeira's ecosystem dynamics such as the endemic Madeira laurel pigeon (Columba trocaz), a key seed-dispersal (Oliveira et al. 2002) or the endemic Madeira-wall lizard (Teira dugesii), an important arthropod predator and pollinator (Esposito et al. 2021) and a key prey for a wide array of native predators (e.g., the Macaronesian Kestrel (Falco tinnunculus canariensis)) (Jesus et al. 2005;Rocha et al. 2010). ...
Invasive mammalian predators are arguably the most damaging group of alien animals for global biodiversity and their impacts are particularly damaging in endemic-rich insular ecosystems. Ferrets (Mustela furo) are well-known for their potential to establish self-sustaining feral populations. Yet, knowledge about their distribution and trophic interactions is scarce. Here, we provide ample evidence of a well-established and widespread population of ferrets on the subtropical island of Madeira (Portugal). Ferrets are using natural and human-dominated habitats, where they are preying on both native (e.g., Cory’s shearwaters (Calonectris borealis) and the endemic and IUCN Endangered Zino’s petrel (Pterodroma madeira)) and non-native vertebrates.
... Rapid advances in high-throughput sequencing technologies over the past decade have opened new avenues for addressing the genetic basis of natural population adaptation and speciation 14 . The use of genetic data has proven valuable in delineating taxa that cannot be identified based on morphology alone [15][16][17] . In the case of endangered animals, the analysis of haplotype can assist in detecting hidden signals of inbreeding depression, providing crucial insights for conservation initiatives 18 . ...
The Proboscidea, which includes modern elephants, were once the largest terrestrial animals among extant species. They suffered mass extinction during the Ice Age. As a unique branch on the evolutionary tree, the Proboscidea are of great significance for the study of living animals. In this study, we generate chromosome-scale and haplotype-resolved genome assemblies for two extant Proboscidea species (Asian Elephant, Elephas maximus and African Savannah Elephant, Loxodonta africana) using Pacbio, Hi-C, and DNBSEQ technologies. The assembled genome sizes of the Asian and African Savannah Elephant are 3.38 Gb and 3.31 Gb, with scaffold N50 values of 130 Mb and 122 Mb, respectively. Using Hi-C technology ~97% of the scaffolds are anchored to 29 pseudochromosomes. Additionally, we identify ~9 Mb Y-linked sequences for each species. The high-quality genome assemblies in this study provide a valuable resource for future research on ecology, evolution, biology and conservation of Proboscidea species.
... Rapid development of high-throughput sequencing technologies during the last decade has opened new avenues to address the genetic basis of adaptation and speciation in natural populations (Vijay et al., 2016). The use of genetic data has proven to be valuable in delimiting taxa that would not have been recognized based on morphology alone (Spinks and Shaffer, 2005;Wenner et al., 2012;Rodríguez et al., 2020). A high-quality genome is a OPEN ACCESS EDITED BY Shi-Yi Chen, Sichuan Agricultural University, China valuable genetic resource to explore the possible genetic basis for the biological features of lizards (Alföldi et al., 2011;Lind et al., 2019;Gemmell et al., 2020). ...
... To avoid mortality, rescue campaigns are coordinated and implemented by NGOs, citizens, and/or governments to give a second chance to grounded birds (Rodr ıguez et al., 2017). Data coming from rescue campaigns can provide information on the continued survival of rare species (Le Corre et al., 2003;Rodr ıguez et al., 2020), the potential locations of their breeding colonies (Barros et al., 2018(Barros et al., , 2019, and as a proxy to infer breeding population size and population trends (Rodr ıguez, Rodr ıguez & Lucas, 2012; Ainley, Schneider & Spencer, 2023;Chevillon et al., 2022). ...
... Cryptic speciation refers to the genetic divergence of species with little or no morphological differentiation. This process is widespread in Procellariformes, including albatrosses (Eda et al. 2020, Abeyrama et al. 2021, shearwaters (Rodríguez et al. 2020), and storm petrels (Taylor et al. 2018). Due to a lack of clearly discernable morphological differences, most cryptic bird species have been described only recently, aided by the advent of molecular techniques. ...
... To illustrate our poor knowledge of the biology of some of the species affected by the fallout, I highlight the recent description of an endemic subspecies of one of the most studied seabirds, the Manx Shearwater. The endemic taxon was described using mostly specimens and individuals grounded by light pollution on the Canaries, Madeira, Azores, and United Kingdom (Rodríguez et al., 2020). ...
The attraction of seabirds to artificial lights leads to fallout and mortality events involving, in some cases, thousands of birds in a single breeding season. To mitigate light pollution-induced mortality the most common action is the rescue programs, but these programs rescue already grounded birds and do not address the cause of the problem. This chapter provides a summary of the mitigation actions to reduce the ecological consequences of light pollution based on the following management options, namely to (i) avoid or prevent the use of artificial light; (ii) limit the duration of lighting; (iii) reduce light spill; (iv) reduce the intensity of lighting; and (v) change light spectral composition. Finally, knowledge gaps and future research to better understand and mitigate this threat are identified. These are (i) the estimation of mortality and effects on populations; (ii) determination of threshold light levels and safe distances from light sources; (iii) documentation of the fate of rescued birds; (iv) improvement in rescue programs; and (v) research on seabird-friendly lights to minimize the attraction.
... The Canaries are an active volcanic archipelago that started to form several million years ago (Anguita and Hernán 2000) about 100 km from the coast of north-western Africa and was never connected to the mainland. This long-term isolation (Norder et al. 2019), along with its subtropical climate and elevation gradients (Steinbauer et al. 2016), has resulted in a high level of endemicity, for example in plants (Carine et al. 2009), reptiles (Thorpe andBaez 1993;Nogales et al. 1998;Nogales et al. 2001;Molina-Borja 2003;Mateo et al. 2011), mammals (Hutterer et al. 1987;Pestano et al. 2003;Firmat et al. 2010;Masseti 2010) and birds (Illera et al. 2016;Lifjeld et al. 2016;Rodríguez et al. 2020;Senfeld et al. 2020). Among them, an endemic barn owl subspecies, T. a. gracilirostris (Hartert 1905), has been described based on its morphological traits, especially for its smaller size and darker coloration (Bannerman 1963;Clements et al. 2019). ...
Islands, and the particular organisms that populate them, have long fascinated biologists. Due to their isolation, islands offer unique opportunities to study the effect of neutral and adaptive mechanisms in determining genomic and phenotypical divergence. In the Canary Islands, an archipelago rich in endemics, the barn owl (Tyto alba), present in all the islands, is thought to have diverged into a subspecies (T. a. gracilirostris) on the eastern ones, Fuerteventura and Lanzarote. Taking advantage of 40 whole-genomes and modern population genomics tools, we provide the first look at the origin and genetic makeup of barn owls of this archipelago. We show that the Canaries hold diverse, long-standing and monophyletic populations with a neat distinction of gene pools from the different islands. Using a new method, less sensitive to structure than classical FST, to detect regions involved in local adaptation to insular environments, we identified a haplotype-like region likely under selection in all Canaries individuals and genes in this region suggest morphological adaptations to insularity. In the eastern islands, where the subspecies is present, genomic traces of selection pinpoint signs of adapted body proportions and blood pressure, consistent with the smaller size of this population living in a hot arid climate. In turn, genomic regions under selection in the western barn owls from Tenerife showed an enrichment in genes linked to hypoxia, a potential response to inhabiting a small island with a marked altitudinal gradient. Our results illustrate the interplay of neutral and adaptive forces in shaping divergence and early onset speciation.
... Other endangered procellariiform species, such Bulwer's petrel Bulweria bulwerii, the Manx Shearwater Puffinus puffinus or the Macaronesian Shearwater Puffinus baroli, together with other endemic species (e.g. land snails, lizards, and plants), would also benefit from predator control and environmentally conscious human development (Medina & Nogales, 2009;Traveset et al., 2009;Rodríguez et al., 2020). further studies of the interplay between threats, such as rat and cat predation, light pollution, plastic ingestion, bycatch or tourism, on shearwater demographic and breeding success are needed. ...
Procellariiformes are one of the most threatened groups of birds of the world so knowledge of nesting habitat and factors affecting breeding rates are vital issues for their conservation. Although Cory's Shearwater Calonectris borealis is a well-studied seabird species on the whole, information on the relationship between its breeding parameters and nest site characteristics is quite limited. To address this gap, during 2017-2019, we conducted a study on its breeding performance on Tenerife, the largest and the most densely populated island of the Canarian archipelago. We constructed generalized linear mixed models to evaluate the potential effects of nest features on breeding performance. Two variables explained breeding success: the distance from the nest to the nearest paved road, and the presence of pebbles at the entrance of the nest-burrow, which correlated negatively and positively with breeding success, respectively. The majority of failures occurred during the incubation period. Breeding failures were mainly related to egg abandonment and rat predation upon eggs or chicks. Effective measures mitigating human-instigated disturbance (e.g. control of dogs, rats and feral cat populations, and reducing light pollution), together with studies on factors affecting demographic parameters, are needed to guarantee the long-term conservation of Cory's Shearwater and other seabird species on the main Canary Islands.
... Three main approaches aim to address current shortcomings and improve the overall management of light pollution: knowledge, dissemination, and mitigation & urban planning. [4] Yes. Here we present a general overview of the methods and current results from the main actions executed during the project and generally discuss its effectiveness and implications to the region. ...
Any efforts to conduct a sustainable management of urban and natural landscapes benefit from an interdisciplinary approach and active collaboration between actors, thus increasing the feasibility and effectiveness of the proposed actions. With the emergent transition of urban lighting to white LED technology, such shifts can bring a variety of negative effects to these environments, thus such actions should be applied taking into account as broad a knowledge set as available. These are often fragmented and incoherent thus in need of actions which unite them into usable and common tools. In the North Atlantic region of Macaronesia, a project has been implemented which uses the negative effects light pollution has on seabird populations as a base to effect changes in the regional lighting schemes, decreasing light pollution and increasing the sustainability of the current LED transition, improving practices and awareness, to the benefit of both seabirds and human populations alike.
Many highly recognisable species lack genetic data important for conservation due to neglect over their hyperabundance. This likely applies to the Sulphur-crested Cockatoo (Cacatua galerita), one of the world’s most iconic parrots. The species is native to Australia, New Guinea and some surrounding Melanesian islands. Four subspecies are currently recognised based on morphology. Australian subspecies and populations are abundant, but several factors threaten those in New Guinea and Melanesia. Genetic data from natural populations are scarce – information that is vital to identifying evolutionarily significant units (ESUs) important for modern conservation planning. We used whole-genome resequencing to investigate patterns of differentiation, evolutionary affinities and demographic history across C. galerita’s range to assess whether currently recognised subspecies represent ESUs. We complement this with an assessment of bioacoustic variation across the species’ distribution range. Our results point to C. galerita sensu lato (s.l.) comprising two species. We restrict C. galerita sensu stricto (s.s.) to populations in Australia and the Trans-Fly ecodomain of southern New Guinea. The second species, recognised here as Cacatua triton, likely occurs over much of the rest of New Guinea. Restricting further discussion of intraspecific diversity in C. triton, we show that within C. galerita s.s. two ESUs exist, which align to Cacatua galerita galerita in eastern Australia and southern New Guinea and Cacatua galerita fitzroyi in northern and north-western Australia. We suggest that the evolution of these species and ESUs are linked to Middle and Late Pleistocene glacial cycles and their effects on sea level and preferential habitats. We argue that conservation assessments need updating, protection of preferential forest and woodland habitats are important and reintroductions require careful management to avoid possible negative hybridization effects of non-complementary lineages.
Mammalian predators introduced to oceanic islands pose a significant threat to biodiversity and have led to numerous extinctions. Free‐ranging cats are particularly problematic due to their predatory habits and negative impact on conservation. However, there is limited information on the ecology and population status of free‐ranging cats in insular ecosystems, where they often represent the apex terrestrial predator. Using a peri‐urban protected area in the subtropical island of Madeira as a case study, we employed camera traps to assess the density of free‐ranging cats and investigate the ecological drivers influencing their abundance and activity in nonurban insular habitats. Based on 582 trapping‐nights, we identified 25 individual cats from 156 cat detections. Spatially explicit capture–recapture models revealed a density of 1.4 cats per km ² . Cat activity was positively affected by both the proportion of rocky areas in the landscape and the distance to human resource subsidies, whereas no significant driver was found for abundance. Our results indicate that cats are highly abundant throughout the protected area and suggest that their core home ranges are associated with rocky terrain, away from the most humanized sections of the park. Free‐ranging cats do not appear to heavily rely on anthropogenic food sources, signaling that they may rely mostly on wild prey to fulfill their dietary needs. Their preference for rocky areas could be explained by the increased availability of shelter and prey, such as the Madeira wall lizard ( Teira dugesii ). Notably, cat abundance and activity were particularly high in the vicinity of the only known breeding colony of the locally threatened Manx shearwater ( Puffinus puffinus ) on Madeira Island. Our findings suggest that cats pose a significant threat to the native vertebrate fauna of the protected area and thus their management, particularly during the breeding season of the Manx shearwater, should be considered.
Combining genetic and ecological measures of differentiation can provide compelling evidence for ecological and genetic divergence among lineages. The Rough-footed Mud Turtle, Kinosternon hirtipes, is distributed from the Trans-Pecos region of Texas to the highlands of Central Mexico and contains six described subspecies, five of which are extant. We use ddRAD sequencing and species distribution models to assess levels of ecological and genetic differentiation among these subspecies. We also predict changes in climatically suitable habitat under different climate change scenarios and assess levels of genetic diversity and inbreeding within each lineage. Our results show that there is strong genetic and ecological differentiation among multiple lineages within K. hirtipes, and that this differentiation appears to be the result of vicariance associated with the Trans-Mexican Volcanic Belt. We propose changes to subspecies designations to more accurately reflect the evolutionary relationships among populations and assess threats to each subspecies.
There is increasing evidence for impacts of light pollution on the physiology and behaviour of wild animals. Nocturnally active Procellariiform seabirds are often found grounded in areas polluted by light and struggle to take to the air again without human intervention. Hence, understanding their responses to different wavelengths and intensities of light is urgently needed to inform mitigation measures. Here, we demonstrate how different light characteristics can affect the nocturnal flight of Manx shearwaters Puffinus puffinus by experimentally introducing lights at a colony subject to low levels of light pollution due to passing ships and coastal developments. The density of birds in flight above the colony was measured using a thermal imaging camera. We compared number of flying shearwaters under dark conditions and in response to an artificially introduced light, and observed fewer birds in flight during ‘light-on’ periods, suggesting that adult shearwaters were repelled by the light. This effect was stronger with higher light intensity, increasing duration of ‘light-on’ periods and with green and blue compared to red light. Thus, we recommend lower light intensity, red colour, and shorter duration of ‘light-on’ periods as mitigation measures to reduce the effects of light at breeding colonies and in their vicinity.
An updated version of the checklist of birds of Brazil is presented, along with a summary of the changes approved by the Brazilian Ornithological Records Committee’s Taxonomy Subcommittee since the first edition, published in 2015. In total, 1971 bird species occurring in Brazil are supported by documentary evidence and are admitted to the Primary List, 4.3% more than in the previous edition. Eleven additional species are known only from undocumented records (Secondary List). For each species on the Primary List, status of occurrence in the country is provided and, in the case of polytypic species, the respective subspecies present in Brazilian territory are listed. Explanatory notes cover taxonomic changes, nomenclatural corrections, new occurrences, and other changes implemented since the last edition. Ninety species are added to the Primary List as a result of species descriptions, new occurrences, taxonomic splits, and transfers from the Secondary List due to the availability of documentation. In contrast, eight species are synonymized or assigned subspecific status and thus removed from the Primary List. In all, 293 species are endemic to Brazil, ranked third among the countries with the highest rate of bird endemism. The Brazilian avifauna currently consists of 1742 residents or breeding migrants, 126 seasonal non-breeding visitors, and 103 vagrants. The category of vagrants showed the greatest increase (56%) compared to the previous list, mainly due to new occurrences documented in recent years by citizen scientists. The list updates the diversity, systematics, taxonomy, scientific and vernacular nomenclature, and occurrence status of birds in Brazil.
High numbers of threatened species might be expected to occur where overall species richness is also high; however, this explains only a proportion of the global variation in threatened species richness. Understanding why many areas have more or fewer threatened species than would be expected given their species richness, and whether that is consistent across taxa, is essential for identifying global conservation priorities. Here, we show that, after controlling for species richness, environmental factors, such as temperature and insularity, are typically more important than human impacts for explaining spatial variation in global threatened species richness. Human impacts, nevertheless, have an important role, with relationships varying between vertebrate groups and zoogeographic regions. Understanding this variation provides a framework for establishing global conservation priorities, identifying those regions where species are inherently more vulnerable to the effects of threatening human processes, and forecasting how threatened species might be distributed in a changing world. Understanding to what extent geographic patterns in threatened species diversity are driven by environmental features or human activities could aid conservation. Here, Howard et al. investigate broad scale patterns in species richness of threatened vertebrates and test the role of environmental and anthropogenic drivers.
Elucidating the factors underlying the origin and maintenance of genetic variation among populations is crucial for our understanding of their ecology and evolution, and also to help identify conservation priorities. While intrinsic movement has been hypothesized as the major determinant of population genetic structuring in abundant vagile species, growing evidence indicates that vagility does not always predict genetic differentiation. However, identifying the determinants of genetic structuring can be challenging, and these are largely unknown for most vagile species. Although, in principle, levels of gene flow can be inferred from neutral allele frequency divergence among populations, underlying assumptions may be unrealistic. Moreover, molecular studies have suggested that contemporary gene flow has often not overridden historical influences on population genetic structure, which indicates potential inadequacies of any interpretations that fail to consider the influence of history in shaping that structure. This exhaustive review of the theoretical and empirical literature investigates the determinants of population genetic differentiation using seabirds as a model system for vagile taxa. Seabirds provide a tractable group within which to identify the determinants of genetic differentiation, given their widespread distribution in marine habitats and an abundance of ecological and genetic studies conducted on this group. Herein we evaluate mitochondrial DNA (mtDNA) variation in 73 seabird species. Lack of mutation-drift equilibrium observed in 19% of species coincided with lower estimates of genetic differentiation, suggesting that dynamic demographic histories can often lead to erroneous interpretations of contemporary gene flow, even in vagile species. Presence of land across the species sampling range, or sampling of breeding colonies representing ice-free Pleistocene refuge zones, appear to be associated with genetic differentiation in Tropical and Southern Temperate species, respectively, indicating that long-term barriers and persistence of populations are important for their genetic structuring. Conversely, biotic factors commonly considered to influence population genetic structure, such as spatial segregation during foraging, were inconsistently associated with population genetic differentiation. In light of these results, we recommend that genetic studies should consider potential historical events when identifying determinants of genetic differentiation among populations to avoid overestimating the role of contemporary factors, even for highly vagile taxa.
The diversity of bats worldwide includes large numbers of cryptic species, partly because divergence in acoustic traits such as echolocation calls are under stronger selection than differences in visual appearance in these nocturnal mammals. Island faunas often contain disproportionate numbers of endemic species, and hence we might expect cryptic, endemic species to be discovered relatively frequently in bats inhabiting islands. Species are best defined when multiple lines of evidence supports their diagnosis. Here we use morphometric, acoustic, and molecular phylogenetic data to show that a horseshoe bat in the Andaman Islands is distinct in all three aspects, supporting its status as a distinct species. We recommend investigation into possible new and endemic bat species on islands by using integrated approaches that provide independent lines of evidence for taxonomic distinctiveness. We provide a formal redescription of the taxon newly raised to species level, Rhinolophus andamanensis Dobson, 1872.
Genetic variation is fundamental to population fitness and adaptation to environmental change. Human activities are driving declines in many wild populations and could have similar effects on genetic variation. Despite the importance of estimating such declines, no global estimate of the magnitude of ongoing genetic variation loss has been conducted across species. By combining studies that quantified recent changes in genetic variation across a mean of 27 generations for 91 species, we conservatively estimate a 5.4‐6.5% decline in within‐population genetic diversity of wild organisms since the industrial revolution. This loss has been most severe for island species, which show a 30% average decline. We identified taxonomic and geographic gaps in temporal studies that must be urgently addressed. Our results are consistent with single time‐point meta‐analyses, which indicated that genetic variation is likely declining. However, our results represent the first confirmation of a global decline, and provide an estimate of the magnitude of the genetic variation lost from wild populations.
This article is protected by copyright. All rights reserved.
Shearwaters and petrels (hereafter petrels) are highly adapted seabirds that occur across all the world’s oceans. Petrels are a threatened seabird group comprising 124 species. They have bet-hedging life histories typified by extended chick rearing periods, low fecundity, high adult survival, strong philopatry, monogamy and long-term mate fidelity and are thus vulnerable to change. Anthropogenic alterations on land and at sea have led to a poor conservation status of many petrels with 52 (42%) threatened species based on IUCN criteria and 65 (52%) suffering population declines. Some species are well-studied, even being used as bioindicators of ocean health, yet for others there are major knowledge gaps regarding their breeding grounds, migratory areas or other key aspects of their biology and ecology. We assembled 38 petrel conservation researchers to summarize information regarding the most important threats according to the IUCN Red List of threatened species to identify knowledge gaps that must be filled to improve conservation and management of petrels. We highlight research advances on the main threats for petrels (invasive species at breeding grounds, bycatch, overfishing, light pollution, climate change, and pollution). We propose an ambitious goal to reverse at least some of these six main threats, through active efforts such as restoring island habitats (e.g., invasive species removal, control and prevention), improving policies and regulations at global and regional levels, and engaging local communities in conservation efforts.
Species are the basic currency in biodiversity studies, but what constitutes a species has long been controversial. Since the late 1990s, debates over species have shifted from theoretical questions (e.g., What is a species? Which species concept is best?) to empirical questions (How can we document species both efficiently and accurately?). A growing number of taxonomists agree that species can be discovered and documented in many different ways, preferably by employing and combining multiple types of evidence (“integrative taxonomy”). This chapter examines how and why avian taxonomy has become integrative, how species hypotheses are documented and falsified, and how the growth of taxonomic knowledge provides new and valuable insights into the speciation process, biogeography, and conservation biology.
Unresolved taxonomy of threatened species is problematic for conservation as the field relies on species being distinct taxonomic units. Differences in breeding habitat and results from a preliminary molecular analysis indicated that the New Zealand population of the South Georgian Diving Petrel (Pelecanoides georgicus) was a distinct, yet undescribed, species. We measured 11 biometric characters and scored eight plumage characters in 143 live birds and 64 study skins originating from most populations of P. georgicus, to assess their taxonomic relationships. We analysed differences with principal component analyses (PCA), factorial ANOVAs, and Kruskal-Wallis rank sum tests. Results show that individuals from New Zealand differ significantly from P. georgicus from all other populations as following: 1) longer wings, 2) longer outer tail feathers, 3) deeper bills, 4) longer heads, 5) longer tarsi, 6) limited collar extent, 7) greater extent of contrasting scapulars, 8) larger contrasting markings on the secondaries, 9) paler ear coverts, 10) paler collars, and 11) paler flanks. Furthermore, we used a species delimitation test with quantitative phenotypic criteria; results reveal that the New Zealand population of P. georgicus indeed merits species status. We hereby name this new species Pelecanoides whenuahouensis sp. nov. Due to severe reductions in its range and the very low number of remaining birds (~150 individuals limited to a single breeding colony on Codfish Island/Whenua Hou) the species warrants listing as ‘Critically Endangered’. An abstract in the Māori language/Te Reo Māori can be found in S1 File.
Behavioral changes, such as those involved in mating, foraging, and migration, can generate reproductive barriers between populations. Birds, in particular, are known for their great diversity in these behaviors, and so behavioral isolation is often proposed to be the major driver of speciation. Here, we review empirical evidence to evaluate the importance of behavioral isolation in the early stages of avian speciation. Experimentally measured mating preferences indicate that changes in mating behavior can result in premating barriers, with their strength depending on the extent of divergence in mating signals. Differences in migratory and foraging behavior also can play important roles in generating reproductive barriers in the early stages of speciation. However, because premating behavioral isolation is imperfect, extrinsic postzygotic barriers, in the form of selection against hybrids having intermediate phenotypes, also play an important role in avian diversification, especially in completing the speciation process. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics Volume 49 is November 2, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) (Drummond et al., 2002; Mau et al., 1999; Rannala and Yang, 1996) flourishes as a popular approach to uncover the evolutionary relationships among taxa, such as genes, genomes, individuals or species. MCMC approaches generate samples of model parameter values - including the phylogenetic tree -drawn from their posterior distribution given molecular sequence data and a selection of evolutionary models. Visualising, tabulating and marginalising these samples is critical for approximating the posterior quantities of interest that one reports as the outcome of a Bayesian phylogenetic analysis. To facilitate this task, we have developed the Tracer (version 1.7) software package to process MCMC trace files containing parameter samples and to interactively explore the high-dimensional posterior distribution. Tracer works automatically with sample output from BEAST (Drummond et al., 2012), BEAST2 (Bouckaert et al., 2014), LAMARC (Kuhner, 2006), Migrate (Beerli, 2006), MrBayes (Ronquist et al., 2012), RevBayes (Höhna et al., 2016) and possibly other MCMC programs from other domains.
Taxonomy is a scientific discipline that has provided the universal naming and classification system of biodiversity for centuries and continues effectively to accommodate new knowledge. A recent publication by Garnett and Christidis [1] expressed concerns regarding the difficulty that taxonomic changes represent for conservation efforts and proposed the establishment of a system to govern taxonomic changes. Their proposal to "restrict the freedom of taxonomic action" through governing subcommittees that would "review taxonomic papers for compliance" and their assertion that "the scientific community's failure to govern taxonomy threatens the effectiveness of global efforts to halt biodiversity loss, damages the credibility of science, and is expensive to society" are flawed in many respects. They also assert that the lack of governance of taxonomy damages conservation efforts, harms the credibility of science, and is costly to society. Despite its fairly recent release, Garnett and Christidis' proposition has already been rejected by a number of colleagues [2,3,4,5,6,7,8]. Herein, we contribute to the conversation between taxonomists and conservation biologists aiming to clarify some misunderstandings and issues in the proposition by Garnett and Christidis.
Grounding of thousands of newly fledged petrels and shearwaters (family Procellariidae) in built-up areas due to artificial light is a global problem. Due to their anatomy these grounded birds find it difficult to take off from built-up areas, and many fall victim to predation, cars, dehydration or starvation. This research investigated a combination of several factors that may influence the number of Manx Shearwater Puffinus puffinus groundings in a coastal village of Scotland located close to a nesting site for this species. A model was developed that used meteorological variables and moon cycle to predict the daily quantity of birds that were recovered on the ground. The model, explaining 46.32% of the variance of the data, revealed how new moon, and strong onshore winds influence grounding. To a lesser extent, visibility conditions can also have an effect on grounding probabilities. The analysis presented in this study can improve rescue campaigns of not only Manx Shearwaters but also other species attracted to the light pollution by predicting conditions leading to an increase in the number of groundings. It could also inform local authorities when artificial light intensity needs to be reduced.
Extinctions have altered island ecosystems throughout the late Quaternary. Here, we review the main historic drivers of extinctions on islands, patterns in extinction chronologies between islands, and the potential for restoring ecosystems through reintroducing extirpated species. While some extinctions have been caused by climatic and environmental change, most have been caused by anthropogenic impacts. We propose a general model to describe patterns in these anthropogenic island extinctions. Hunting, habitat loss and the introduction of invasive predators accompanied prehistoric settlement and caused declines of endemic island species. Later settlement by European colonists brought further land development, a different suite of predators and new drivers, leading to more extinctions. Extinctions alter ecological networks, causing ripple effects for islands through the loss of ecosystem processes, functions and interactions between species. Reintroduction of extirpated species can help restore ecosystem function and processes, and can be guided by palaeoecology. However, reintroduction projects must also consider the cultural, social and economic needs of humans now inhabiting the islands and ensure resilience against future environmental and climate change.
Artificial lights at night cause high mortality of seabirds, one of the most endangered groups of birds globally. Fledglings of burrow-nesting seabirds, and to a lesser extent adults, are grounded by lights when they fly at night. We review the current state of knowledge of light attraction, identify information gaps and propose measures to address the problem. Although other avian families such as Alcidae and Anatidae can be involved, the most affected seabirds are petrels and shearwaters: at least 56 species, more than one-third of them (24) threatened, are grounded by lights. Grounded seabirds have been found worldwide, mainly on oceanic islands but also at some continental locations. Petrel breeding grounds confined to formerly uninhabited islands are particularly at risk from ever-growing levels of light pollution due to tourism and urban sprawl. Where it is impractical to ban external lights, rescue programs of grounded birds offer the most immediate and extended mitigation measures to reduce light-induced mortality, saving thousands of birds every year. These programs also provide useful information for seabird management. However, the data typically are fragmentary and often strongly biased so the phenomenon is poorly understood, leading to inaccurate impact estimates. We identified as the most urgent priority actions: 1) estimation of mortality and impact on populations; 2) assessment of threshold light levels and safe distances from light sources; 3) documenting the fate of rescued birds; 4) improvement of rescue campaigns, particularly in terms of increasing recovery rates and level of care; and 5) research on seabird-friendly lights to reduce attraction. More research is necessary to improve our understanding of this human-wildlife conflict and to design effective management and mitigation measures. This article is protected by copyright. All rights reserved
Oceanic islands are excellent systems for allowing biologists to test evolutionary hypotheses due to their relative simplicity of habitats, naturally replicated study design and high levels of endemic taxa with conspicuous variation in form, colour and behaviour. Over the last two decades the Canary Islands archipelago has proved an ideal system for evolutionary biologists who seek to unravel how biodiversity arises and disappears. In this review we have evaluated the contribution of the study of Canarian birds to our understanding of how and why species occur and change over time. We focus our attention on both extant and extinct Canarian taxa, and describe how research on these species has filled gaps in our understanding of avian speciation and extinction. In addition, we discuss the necessity of revising the current taxonomy in the Canarian avian taxa, especially the status of the endemic subspecies, some of which might be better treated as full species. An accurate classification of Canarian birds is not only necessary for testing evolutionary, biogeographic and ecological hypotheses, but also for effective decision making about conservation and environmental management. Finally we introduce future avenues of research that we feel will yield the most exciting and promising findings on island evolution in the coming years.
This article presents W-IQ-TREE, an intuitive and user-friendly web interface and server for IQ-TREE, an efficient phylogenetic
software for maximum likelihood analysis. W-IQ-TREE supports multiple sequence types (DNA, protein, codon, binary and morphology)
in common alignment formats and a wide range of evolutionary models including mixture and partition models. W-IQ-TREE performs
fast model selection, partition scheme finding, efficient tree reconstruction, ultrafast bootstrapping, branch tests, and
tree topology tests. All computations are conducted on a dedicated computer cluster and the users receive the results via
URL or email. W-IQ-TREE is available at http://iqtree.cibiv.univie.ac.at. It is free and open to all users and there is no login requirement.
Light pollution and its consequences on ecosystems are increasing worldwide. Knowledge on the threshold levels of light pollution at which significant ecological impacts emerge and the size of dark refuges to maintain natural nocturnal processes is crucial to mitigate its negative consequences. Seabird fledglings are attracted by artificial lights when they leave their nest at night, causing high mortality. We used GPS data-loggers to track the flights of Cory’s shearwater Calonectris diomedea fledglings from nest-burrows to ground, and to evaluate the light pollution levels of overflown areas on Tenerife, Canary Islands, using nocturnal, high-resolution satellite imagery. Birds were grounded at locations closer than 16 km from colonies in their maiden flights, and 50% were rescued within a 3 km radius from the nest-site. Most birds left the nests in the first three hours after sunset. Rescue locations showed radiance values greater than colonies, and flight distance was positively related to light pollution levels. Breeding habitat alteration by light pollution was more severe for inland colonies. We provide scientific-based information to manage dark refuges facilitating that fledglings from inland colonies reach the sea successfully. We also offer methodological approaches useful for other critically threatened petrel species grounded by light pollution.
Phylogenetic methods increasingly are brought to bear on questions of subspecies taxonomy, but several recent examples highlight the need for a clear and consistent philosophical approach to how genetic data are used to assess subspecies limits. Such standards are crucial conceptually, whether or not taxonomic decisions affect conservation decisions, as they might in a recent study focused on the California Gnatcatcher (Polioptila californica), a taxon currently protected under the U.S. Endangered Species Act. It is also crucial that any adopted framework allows each of a full range of alternatives to be either supported or rejected. In this spirit, in addition to recommending best practices, I propose an amendment to the phylogenetic species concept to include a subspecies category.
Townsend’s Shearwater (Puffinus
auricularis auricularis) is a highly threatened bird and currently breeds on Socorro and Clarión Islands, México. This subspecies has minor differences in plumage patterns when compared to Newell’s Shearwater of Hawaii (USA) (Puffinus auricularis newelli). These two forms are recognized as subspecies by the American Ornithologist’s Union. However, some authors consider them as distinct species based on subtle plumage differences and different breeding chronologies. We used Bayesian and Maximum Likelihood methods to compare the cytochrome
b and cytochrome oxidase I sequences from Townsend’s Shearwaters with archived mitochondrial sequences from other taxa in the genus Puffinus. Townsend’s and Newell’s Shearwaters show little genetic differentiation; hence, there is no justification to consider them as different species. Additionally, differences in morphology and ecology might be the result of founder effects and phenotypic plasticity; proven migratory potential provides support to the current taxonomic assessment that considers these birds as conspecifics. We recommend the continued treatment of Townsend’s and Newell’s Shearwaters as two subspecies of P. auricularis. We also advocate treating the Rapa Shearwater (P. myrtae) as a distinct species.
This paper reports the first comprehensive surveys of Fea's Petrel (Pterodroma feae), Bulwer's Petrel (Bulweria bulwerii), Manx Shearwater (Puffinus puffinus), Little Shearwater (Puffinus assimilis baroli) and two temporally-segregated forms of Band-rumped Storm-petrel (Oceanodroma castro) in the whole Azores archipelago, conducted from 1996 to 1998. Listening to nocturnal vocalizations was the main survey method. Breeding of Fea's Petrel was not confirmed and new sites of Bulwer's Petrel were not found (previous status: one site, 50 pairs), but previously undocumented colonies were identified for the remaining species. Manx Shearwater occurred in four colonies with 115-235 pairs (previous status: probable breeder), Little Shearwater occurred in 28 colonies with 840-1,530 pairs (previously: four locations, > 150 pairs), hot-season Band-rumped Storm-petrels occurred in 5 colonies with 250-300 pairs (previously: two locations, 200 pairs) and cool-season Band-rumped Storm-petrels were found in eight locations with 665-740 pairs (previously: three locations, 600 pairs). Most colonies were confined to precipitous cliffs and islets, which may be a result of predation threats by introduced mammals. Although these surveys provided a valuable revision of the status and distribution for these species of conservation concern, further survey work is warranted and target areas are indicated. We discuss the potential and limitations of listening for nocturnal vocalizations as a method to survey and monitor shearwater and petrel populations in inaccessible habitats.
Dissatisfaction with the subspecies unit of classification is, in part, a consequence of the failure of many of those who have described subspecies to follow the conceptual definition of the subspecies, namely that it should represent diagnosable units. The antiquity of the descriptions of most subspecies (median year of description of currently recognized subspecies estimated to be 1908–1909) means that the majority predated any statistical tools for assessing diagnosability. The traditional subspecies concept, as originally construed, identifies minimum diagnosable units as terminal taxa, and I suggest that it is thus essentially synonymous with the phylogenetic species concept. Therefore, both must deal with the fundamental difficulties inherent in using diagnosability as a criterion. Application of monophyly as a criterion for taxon rank at the population level has inherent difficulties. An advantage of the biological species concept is that it incorporates, in its classification of taxa, ass...
Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast
programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus,
there is need for additional approaches that employ different search strategies to find ML trees and that are at the same
time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation
method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found
higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use
the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein
alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3–97.1%. IQ-TREE
is freely available at http://www.cibiv.at/software/iqtree.
Introduction
Seabirds have been historically used to monitor environmental contamination. The aim of the present study was to test the suitability of a species belonging to the Procellariiformes group, the Manx shearwater, Puffinus puffinus, as a sentinel of environmental health, by determining contaminant levels (trace metals and organochlorine compounds) from carcass tissues and by isolating Vibrio spp. and Aeromonas spp. from live specimens. To this end, 35 Puffinus puffinus carcasses wrecked on the north-central coast of the state of Rio de Janeiro, Brazil, and two carcasses recovered in Aracruz, on the coast of the state of Espírito Santo, Brazil, were sampled, and fragments of muscle and hepatic tissues were collected for contaminant analyses. Swabs from eleven birds found alive at the north-central coast of Rio de Janeiro were collected for isolation of the aforementioned bacteria.
Results
The average concentration in dry weight (dw) of the trace metals were: mercury 7.19 mg kg-1(liver) and 1.23 mg kg-1 (muscle); selenium 34.66 mg kg-1 (liver) and 7.98 mg kg-1 (muscle); cadmium 22.33 mg kg-1 (liver) and 1.11 mg kg-1 (muscle); and lead, 0.1 mg kg--1 (liver) and 0.16 mg kg-1 (muscle). Organochlorine compounds were detected in all specimens, and hexachlorbiphenyls, heptachlorbiphenyls and DDTs presented the highest levels. Regarding microbiological contamination, bacteria from the Vibrio genus were isolated from 91% of the analyzed specimens. Vibrio harveyi was the predominant species. Bacteria from the Aeromonas genus were isolated from 18% of the specimens. Aeromonas sobria was the only identified species.
Conclusions
The results indicate that Puffinus puffinus seems to be a competent ocean health sentinel. Therefore, the monitoring of contaminant levels and the isolation of public health interest bacteria should proceed in order to consolidate this species importance as a sentinel.
We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular BEAST 1 platform to correct structural deficiencies that became evident as the BEAST 1 software evolved. Key among those deficiencies was the lack of post-deployment extensibility. BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform. This package architecture is showcased with a number of recently published new models encompassing birth-death-sampling tree priors, phylodynamics and model averaging for substitution models and site partitioning. A second major improvement is the ability to read/write the entire state of the MCMC chain to/from disk allowing it to be easily shared between multiple instances of the BEAST software. This facilitates checkpointing and better support for multi-processor and high-end computing extensions. Finally, the functionality in new packages can be easily added to the user interface (BEAUti 2) by a simple XML template-based mechanism because BEAST 2 has been re-designed to provide greater integration between the analysis engine and the user interface so that, for example BEAST and BEAUti use exactly the same XML file format.
Estimating genealogical relationships among genes at the population level presents a number of difficulties to traditional methods of phylogeny reconstruction. These traditional methods such as parsimony, neighbour-joining, and maximum-likelihood make assumptions that are invalid at the population level. In this note, we announce the availability of a new software package, TCS, to estimate genealogical relationships among sequences using the method of Templeton et al. (1992) .
Nonparametric bootstrap has been a widely used tool in phylogenetic analysis to assess the clade support of phylogenetic trees.
However, with the rapidly growing amount of data, this task remains a computational bottleneck. Recently, approximation methods
such as the RAxML rapid bootstrap (RBS) and the Shimodaira–Hasegawa-like approximate likelihood ratio test have been introduced
to speed up the bootstrap. Here, we suggest an ultrafast bootstrap approximation approach (UFBoot) to compute the support
of phylogenetic groups in maximum likelihood (ML) based trees. To achieve this, we combine the resampling estimated log-likelihood
method with a simple but effective collection scheme of candidate trees. We also propose a stopping rule that assesses the
convergence of branch support values to automatically determine when to stop collecting candidate trees. UFBoot achieves a
median speed up of 3.1 (range: 0.66–33.3) to 10.2 (range: 1.32–41.4) compared with RAxML RBS for real DNA and amino acid alignments,
respectively. Moreover, our extensive simulations show that UFBoot is robust against moderate model violations and the support
values obtained appear to be relatively unbiased compared with the conservative standard bootstrap. This provides a more direct
interpretation of the bootstrap support. We offer an efficient and easy-to-use software (available at http://www.cibiv.at/software/iqtree) to perform the UFBoot analysis with ML tree inference.
In general Manx Shearwaters in the Irish Sea remain faithful to their native colonies, though ringing records indicate a few exceptions. The author considers some evolutionary aspects of the faithfulness to colonies shown by this and other sea-birds.
We present the first objective quantitative assessment of the threats to all 359 species of seabirds, identify the main challenges facing them, and outline priority actions for their conservation. We applied the standardised Threats Classification Scheme developed for the IUCN Red List to objectively assess threats to each species and analysed the data according to global IUCN threat status, taxonomic group, and primary foraging habitat (coastal or pelagic). The top three threats to seabirds in terms of number of species affected and average impact are: invasive alien species, affecting 165 species across all the most threatened groups; bycatch in fisheries, affecting fewer species (100) but with the greatest average impact; and climate change/severe weather, affecting 96 species. Overfishing, hunting/trapping and disturbance were also identified as major threats to seabirds. Reversing the top three threats alone would benefit two-thirds of all species and c. 380 million individual seabirds (c. 45% of the total global seabird population). Most seabirds (c. 70%), especially globally threatened species, face multiple threats. For albatrosses, petrels and penguins in particular (the three most threatened groups of seabirds), it is essential to tackle both terrestrial and marine threats to reverse declines. As the negative effects of climate change are harder to mitigate, it is vital to compensate by addressing other major threats that often affect the same species, such as invasive alien species, bycatch and overfishing, for which proven solutions exist.
Gloger's rule is an ecogeographical rule that links animal colouration with climatic variation. This rule is named after C.W.L. Gloger who was one of the first to summarise the associations between climatic variation and animal colouration, noting in particular that birds and mammals seemed more pigmented in tropical regions. The term ‘Gloger's rule' was coined by B. Rensch in 1929 and included different patterns of variation from those described by Gloger. Rensch defined the rule in two ways: a simple version stating that endothermic animals are predicted to be darker in warmer and humid areas due to the increased deposition of melanin pigments; and a complex version that includes the differential effects of humidity and temperature on both main types of melanin pigments – eu‐ and phaeo‐melanin. The blackish eu‐melanins are predicted to increase with humidity, and decrease only at extreme low temperatures, while the brown‐yellowish phaeomelanins prevail in dry and warm regions and decrease rapidly with lower temperatures. A survey of the literature indicates that there is considerable variation/confusion in the way Gloger's rule is understood (based on 271 studies that define the rule). Whereas the complex version is hardly mentioned, only a quarter of the definitions are consistent with the simple version of Gloger's rule (darker where warm and wet), and most definitions mention only the effects of humidity (darker where wet). A smaller subset of studies define the rule based on other correlated climatic and environmental variables such as vegetation, latitude, altitude, solar radiation, etc., and a few even contradict the original definition (darker where cold). Based on the literature survey, I synthesised the qualitative (N = 124 studies) and quantitative (meta‐analytically, N = 38 studies, 241 effects) evidence testing the simple version of Gloger's rule (I found no tests of the complex version). Both lines of evidence supported the predicted effects of humidity (and closely linked variables) on colour variation, but not the effects of temperature. Moreover, humidity effects are not restricted to birds and mammals, as the data indicate that these effects also apply to insects. This suggests that the simple version of Gloger's rule as originally defined may not be valid, and possibly that the rule should be re‐formulated in terms of humidity effects only. I suggest, however, that more data are needed before such a reformulation, due to potential publication biases. In conclusion, I recommend that authors cite Rensch when referring to Gloger's rule and that they make clear which version they are referring to. Future research should concentrate on rigorously testing the validity and generality of both versions of Gloger's rule and establishing the mechanism(s) responsible for the patterns it describes. Since humidity seems to be the core climatic variable behind Gloger's rule, I suggest that the two most plausible mechanisms are camouflage and protection against parasites/pathogens, the latter possibly through pleiotropic effects on the immune system. Understanding the processes that lead to climatic effects on animal colouration may provide insights into past and future patterns of adaptation to climatic change.
Puffinus lherminieri bannermani is a small black-and-white shearwater, which is endemic to the Ogasawara Islands, Japan. The taxonomic position of this shearwater is contentious. It is treated as a subspecies of Audubon's Shearwater P. lherminieri or the Tropical Shearwater P. bailloni in some checklists, while it is as considered monotypic, as Bannerman's Shearwater P. bannermani, in others. We examined the mitochondrial cytochrome b region to determine the taxon's phylogenetic position. While on the one hand the results showed that it was not genetically related to either P. lherminieri or P. bailloni, but formed a clade with P. myrtae, P. newelli, and P. auricularis, on the other hand, bannermani has diverged substantially from the other three taxa in both genetic and morphological features. This shearwater was first described as Bannerman's Shearwater, and our results confirm that P. lherminieri bannermani should be split from Audubon's Shearwater, and the monotypic Bannerman's Shearwater is recommended to be restored as a distinct species.
The island of Kaua'i, Hawaii, USA, holds a large breeding populations of the endangered Hawaiian Petrel (Pterodroma sandwichensis) and a majority of the world population of the threatened Newell's Shearwater (Puffinus newelli). We evaluated island-wide population trends of both species. For Newell's Shearwaters, we considered radar counts at 13 sites between 1993 and 2013 and annual island-wide tallies of fledglings retrieved after being grounded by light attraction in 1979-2015 (Save Our Shearwaters [SOS] program). For Hawaiian Petrels, we considered radar counts alone. Radar data indicated a 78% decline overall in numbers of Hawaiian Petrels (at an average rate of 6% per year) and a 94% decline overall in numbers of Newell's Shearwaters (at an average rate of 13% per year) during the survey period. Most (92%) radar sites showed significant declines of Newell's Shearwaters across the entire survey period, as did 62% of sites for Hawaiian Petrels. The SOS recovery effort collected 30,522 Newell's Shearwater fledglings between 1979 and 2015. When we compared this dataset in pre- and post-Hurricane Iniki (September 1992) periods, we found a significant downward trend after Hurricane Iniki, similar to the trend seen in the radar data. The large-scale declines found in this study are not surprising, considering the significant threats facing both species on Kaua'i, which include powerline collisions, light attraction, introduced predators, and habitat modification-threats which were potentially exacerbated after Hurricane Iniki. Improved conservation initiatives and an increased understanding of the various threats facing the 2 species are key to reversing these declines.
This new edition to the classic book by ggplot2 creator Hadley Wickham highlights compatibility with knitr and RStudio. ggplot2 is a data visualization package for R that helps users create data graphics, including those that are multi-layered, with ease. With ggplot2, it's easy to:
• produce handsome, publication-quality plots with automatic legends created from the plot specification
• superimpose multiple layers (points, lines, maps, tiles, box plots) from different data sources with automatically adjusted common scales
• add customizable smoothers that use powerful modeling capabilities of R, such as loess, linear models, generalized additive models, and robust regression
• save any ggplot2 plot (or part thereof) for later modification or reuse
• create custom themes that capture in-house or journal style requirements and that can easily be applied to multiple plots
• approach a graph from a visual perspective, thinking about how each component of the data is represented on the final plot
This book will be useful to everyone who has struggled with displaying data in an informative and attractive way. Some basic knowledge of R is necessary (e.g., importing data into R). ggplot2 is a mini-language specifically tailored for producing graphics, and you'll learn everything you need in the book. After reading this book you'll be able to produce graphics customized precisely for your problems, and you'll find it easy to get graphics out of your head and on to the screen or page. New to this edition:<
• Brings the book up-to-date with ggplot2 1.0, including major updates to the theme system
• New scales, stats and geoms added throughout
• Additional practice exercises
• A revised introduction that focuses on ggplot() instead of qplot()
• Updated chapters on data and modeling using tidyr, dplyr and broom
The importance of sympatric speciation - the evolution of reproductive isolation between co-distributed conspecific individuals - in generating biodiversity is highly controversial. Allochrony, or differences in breeding time (phenology) between conspecific individuals, has the potential to lead to reproductive isolation and therefore speciation. We critically review the literature to test the importance of allochronic speciation over the three time scales over which allochrony can occur - over the day, between seasons, or between years - and explore what is known about genomic mechanisms underlying allochrony in the diverse taxa in which it is found. We found that allochrony can be a key contributor to reproductive isolation, especially if populations have little overlap in breeding time and therefore little potential for gene flow, and may sometimes be the initial or key driver of speciation. Shifts in phenology can be caused by several factors, including a new ecological opportunity, environmental change, or reinforcement. The underlying genomic basis of allochrony has been studied mostly in insects, highlighting the need for genomic studies in other taxa; nonetheless, results to date indicate that several cases of allochrony involve changes in circadian genes. This review provides the first comprehensive discussion of the role of allochrony in speciation, and demonstrates that allochrony as a contributor to divergence may be more widespread than previously thought. Understanding genomic changes and adaptations allowing organisms to breed at new times may be key in light of phenological changes required under climate change. This article is protected by copyright. All rights reserved.
The most studied ecogeographic rule is Bergmann's rule, but aspects of the original paper are often presented incorrectly even though Bergmann (1847) is explicitly cited. The goal of this paper is to 1) summarize the contents of Bergmann's paper, supported by direct translations, and 2) to discuss the main issues surrounding Bergmann's rule based on Bergmann's intentions and early definitions of the rule.
Although Bergmann himself never formulated an explicit rule, based on Bergmann's (1847) intentions and early definitions of Bergmann's rule, Bergmann's rule is: “Within species and amongst closely related species of homeothermic animals a larger size is often achieved in colder climates than in warmer ones, which is linked to the temperature budget of these animals.” Bergmann (1847) assumed that the surface area of an animal is a measure for heat dissipation and an animal's volume a measure of its heat production. As body size increases, an animal's surface area increases less than its volume; however, modifications in morphology and behaviour will also influence the temperature budget. Bergmann hypothesized that when everything but size is equal, the smaller animals should live in warmer areas. This was supported by empirical data on > 300 bird species belonging to 86 genera.
Recommendations for use of the term Bergmann's rule include 1) inclusion of a thermoregulatory mechanism, 2) application only to homoeothermic animals, 3) but to any taxonomic group, 4) tests of the rule should test the assumption that larger animals have to produce less heat to increase body temperatures, and 5) future authors should either go back to the original publication (Bergmann 1847) when referring to it or simply not cite it at all.
Synthesis
Based on Bergmann's (1847) intentions and early definitions, Bergmann's rule is: “Within species and amongst closely related species of homeothermic animals a larger size is often achieved in colder climates than in warmer ones, which is linked to the temperature budget of these animals.” Recommendations for use of the term Bergmann's rule include 1) inclusion of a thermoregulatory mechanism, 2) application only to homoeothermic animals, 3) and to any taxonomic group, 4) tests of the rule should examine whether larger animals have to produce less heat to increase body temperatures, and 5) authors should go back to the original publication (Bergmann 1847) when referring to it.
Although described as a distinct species in 1869, for more than a century now New Zealand's grey-faced petrel (Pterodroma macroptera gouldi Hutton, 1869) has been regarded as a subspecies of the great-winged petrel (P. macroptera A. Smith, 1840). However, several authors have recently questioned whether the taxon once again deserves full species status. Here, we demonstrate that the grey-faced petrel is sufficiently distinct in multiple facets of its biology (including mitochondrial DNA, plumage variation, morphometrics, osteology, vocalizations, external parasites, and feeding and breeding biology) to warrant reinstatement of full species status under the morphological, phylogenetic, and potentially biological species concepts. Moreover, we present new evidence from mitochondrial DNA (cytochrome c oxidase subunit 1 and cytochrome b) that suggests the great-winged petrel is actually more closely related to the white-headed petrel (Pterodroma lessonii Garnot, 1826) than to the grey-faced petrel. The reclassification of grey-faced petrel to full species status raises the degree of seabird endemism in New Zealand to 43%, emphasising the status of the archipelago as a hotspot for seabird diversity.
Motivation:
TCS is a widely-used haplotype network reconstruction software, but lacks the capability of overlapping genetic with geographic structure, which is often a first step in phylogeographic analysis.
Results:
tcsBU is a web-based program that extends the capabilities of TCS, by implementing haplotype classification into an arbitrary user-defined scheme, which is displayed as pie-chart like graphs embedded into the network. Taking advantage of modern graphic libraries, tcsBU also improves the speed at which the final network layout is reached. Networks can be saved as a Scalable Vector Graphics format.
Availability and implementation:
tcsBU is available on-line at http://cibio.up.pt/software/tcsBU/. The source code is freely available from https://github.com/sairum/tcsbu/ under a standard MIT license.
Contact:
amsantos@fc.up.pt.
Three medium-sized Puffinus shearwaters breed in Europe: Manx R puffinus, Yelkouan R yelkouan and Balearic Shearwaters R mauretanicus. These three, considered a single, polytypic species until relatively recently, can be difficult to identify in some situations, notably in a vagrant context. This paper presents a detailed review of the plumage variability of the three taxa; combined with an understanding of structural differences and flight characteristics, this should provide a sound basis for the identification of problematic individuals.
Speciation—the multiplication of species through the evolution of barriers to reproduction between populations—plays a central role in evolution since it enables two or more populations to adapt and evolve independently. However, mechanisms of speciation are notoriously difficult to study and poorly understood. Seabirds provide useful models to investigate factors that may promote or inhibit speciation because their ecology and evolutionary genetics are relatively well understood. Here I review population genetic studies of seabirds to test the importance of six factors with the potential to disrupt gene flow enough to result in speciation. Over 200 studies, including over 100 species, have been published to date. Most show evidence of restrictions in gene flow. Physical (geographic) barriers to dispersal are clearly important: conspecific populations that are separated by large expanses of land or ice show evidence of restricted gene flow, and sister species often are separated by physical barriers to gene flow. However, many species of seabirds show evidence of restrictions in gene flow in the absence of physical barriers to dispersal. Study results indicate that differences in ocean regimes, nonbreeding distributions, foraging distributions during the breeding season, and breeding phenology also can disrupt gene flow enough to lead to speciation. Of these, physical isolation and differences in ocean regime appear to be the most important. Philopatry alone may be sufficient to result in reproductive isolation, but usually it acts in combination with other barriers to gene flow. The effects of many other potential influences on gene flow need to be investigated more thoroughly, including colony distribution/location, wind, interspecific interactions, environmental stability/variability, variation in phenotypic traits associated with mate choice (morphology, behaviour, vocalisations) and intrinsic (genomic) incompatabilities. Recent advances in genome sequencing, especially if used in combination with ecological tools such as geolocators and new methods for data interpretation, are opening exiting new avenues to test the importance of various behavioural, ecological, demographic and genomic factors in reducing or promoting gene flow and so affecting speciation.
Islands make up 5.3% of Earth's land area yet maintain an estimated 19% of bird species, 17% of rodents, 17% of flowering
plants, and 27% of human languages. Species diversity is disproportionately threatened on islands in relation to the islands’
proportion of both global land area and species, with 61% of all extinct species and 37% of all critically endangered species
confined to islands. Languages are disproportionately threatened on islands in relation to land area with 11% of extinct languages
and 25% of critically endangered languages on islands. Islands are a priority area for integrated conservation efforts because
they have 14 times greater density of critically endangered terrestrial species and 6 times greater density of critically
endangered languages than continental areas. Invasive species and habitat loss are the largest threats to island terrestrial
species diversity. Proven management actions can reduce these threats, benefiting both local peoples and species diversity
on islands.
[URL: http://cran.r-project.org/web/packages/effsize/effsize.pdf ]
Small black-and-white shearwaters of the genus Puffinus are distributed globally, and their phylogenetic relationships are complex and uncertain. In 1963 a small shearwater collected at Midway Atoll in the North Pacific Ocean was identified as a Little Shearwater (P. assimilis), but several physical features suggest closer alliance with Audubon's Shearwater (P. lherminieri) and its relatives. Biometrics indicate that the taxon this specimen represents is smaller than any other known shearwater, and phylogenetic analyses indicate it is distinct, with a pair-wise sequence divergence of at least 3.8% from related taxa. We thus propose a new species based on the specimen: Bryan's Shearwater (Puffinus bryani nom. nov.). The breeding and nonbreeding ranges of Bryan's Shearwater are unknown, but a physical resemblance to the North Atlantic boydi (of controversial taxonomic status within Puffinus) suggests an affiliation with subtropical or tropical waters. Bryan's Shearwater is apparently rare and could be threatened by extinction; therefore, additional information is needed to increase our understanding of this taxon and its conservation requirements.
In birds, species identity is one of the most important messages conveyed by vocalizations and is the basis for effective acoustic communication between conspecifics. Acoustic analyses can reveal which acoustic cues signal species identity, that is, the cues that could potentially be used by birds for species recognition, whereas playback experiments aim to determine which cues birds actually use for species recognition. Few studies have compared the acoustic cues used for species-specific recognition between closely related species and between sexes within species. We focused on three shearwater species (Puffinus yelkouan, Puffinus mauretanicus, Calonectris d. diomedea) breeding in the Mediterranean basin. In a previous study we showed that males and females of these three closely related species produce broadband calls strongly modulated in frequency and share a wide range of acoustic features signalling species identity. Here, we investigated whether these birds use similar acoustic cues for species recognition. Playback experiments showed that these cues were more similar between species of the genus Puffinus that rely mainly on frequency modulation than between Puffinus and Calonectris species, the latter using mainly frequency spectrum-related cues. In spite of similarities between the Puffinus species, we found substantial differences, P. mauretanicus being more sensitive to frequency value modification than P. yelkouan. We also found that females of the three species rely on more acoustic parameters to identify species than males. Our results show that the species-specific recognition system can show significant differences between closely related species and between sexes.
