Multiple instances of paraphyletic species and cryptic taxa revealed by mitochondrial and nuclear RAD data for Calandrella larks (Aves: Alaudidae).

The avian genus Calandrella (larks) was recently suggested to be non-monophyletic, and was divided into two genera, of which Calandrella sensu stricto comprises 4-5 species in Eurasia and Africa. We analysed mitochondrial cytochrome b (cytb) and nuclear Restriction-site Associated DNA (RAD) sequences from all species, and for cytb we studied 21 of the 22 recognised subspecies, with the aim to clarify the phylogenetic relationships within the genus and to compare large-scale nuclear sequence patterns with a widely used mitochondrial marker. Cytb indicated deep splits among the currently recognised species, although it failed to support the interrelationships among most of these. It also revealed unexpected deep divergences within C. brachydactyla, C. blanfordi/C. erlangeri, C. cinerea, and C. acutirostris. It also suggested that both C. brachydactyla and C. blanfordi, as presently circumscribed, are paraphyletic. In contrast, most of the many subspecies of C. brachydactyla and C. cinerea were unsupported by cytb, although two populations of C. cinerea were found to be genetically distinct. The RAD data corroborated the cytb tree (for the smaller number of taxa analysed) and recovered strongly supported interspecific relationships. However, coalescence analyses of the RAD data, analysed in SNAPP both with and without an outgroup, received equally strong support for two conflicting topologies. We suggest that the tree rooted with an outgroup - which is not recommended for SNAPP - is more trustworthy, and suggest that the reliability of analyses performed without any outgroup species should be thoroughly evaluated. We also demonstrate that degraded museum samples can be phylogenetically informative in RAD analyses following careful bioinformatic treatment. We note that the genus Calandrella is in need of taxonomic revision.

A comparison of the sampling effectiveness of acoustic recorder, camera trap and point count methods in sampling nocturnal birds in Afrotropical landscapes.

Conservation decisions for bird diversity in the Afrotropics are often based on ecological studies utilizing diurnal bird species likely owing to difficulties associated with sampling nocturnal birds. It is therefore important to compare the sampling effectiveness of some of the available techniques that can be used in nocturnal bird surveys to guide future long-term survey efforts. Thus, we compared the sampling effectiveness of point count, acoustic recorder and camera trap for estimating nocturnal bird species richness and also across habitat types. We surveyed 20 points that were spaced at least 500 m apart in November and December 2021 in the Amurum Forest Reserve and its surroundings in Jos-Nigeria. At each point, we used two camera traps, one at the ground and the other at 2.0 m. We also used one acoustic recorder as well as a 15-min point count during each survey at each point. We encountered 11 nocturnal bird species, primarily nightjars but also owls. While we did not encounter any species with the camera traps, all 11 species were recorded using the acoustic recorder. All species except for Ketupa lacteaus were recorded in point count. Eight species were recorded in the gallery, seven in rocky and nine in savannah. Species richness and estimation using the acoustic recorder and point count were similar across habitat types. We conclude that either point count or acoustic recorders are useful for nocturnal bird surveys in Afrotropical environments. However, the choice of methods should be based on the research questions as some questions may be better answered by a specific method or even a combination of both.

Citizen science mitigates the lack of distributional data on Nigerian birds.

Citizen science projects are expanding globally, with the African continent, particularly Nigeria, registering significant growth. Here, we document and analyse novel operations of the Nigerian Bird Atlas Project (NIBAP), 2015-2022. This project has employed the use of ornithologists, mainly trained at the A. P. Leventis Ornithological Research Institute (APLORI) located in Jos, Nigeria, and its 28 bird clubs established across Nigeria to enlist 827 bird enthusiasts that contribute regular and near real-time data about bird distribution and relative abundance in the country. Interestingly, NiBAP has recorded about 75% of the bird species known from Nigeria in only about 50% of Nigeria's total surface area, including 39 nationally threatened species. The Common Bulbul Pycnonotus barbatus, Laughing Dove Spilopelia senegalensis, and Grey-backed Camaroptera Camaroptera brevicaudata were the most commonly recorded species, while Amurum Forest Reserve, Rennajj Fish Farm, and Obudu Cattle Ranch were the most surveyed sites during the period. Thus, our approach reveals how to increase involvement of nature enthusiasts, ornithologists, and a regional research institute to build local capacity and contribute rich information necessary to alleviate the lack of distributional data about Afrotropical avifauna. We strongly recommend our approach to boost other citizen science projects across Africa and beyond to address the huge lack of biodiversity data, create public awareness, and foster conservation education.

Bushmeat hunting changes regeneration of African rainforests.

To assess ecological consequences of bushmeat hunting in African lowland rainforests, we compared paired sites, with high and low hunting pressure, in three areas of southeastern Nigeria. In hunted sites, populations of important seed dispersers-both small and large primates (including the Cross River gorilla, Gorilla gorilla diehli)-were drastically reduced. Large rodents were more abundant in hunted sites, even though they are hunted. Hunted and protected sites had similar mature tree communities dominated by primate-dispersed species. In protected sites, seedling communities were similar in composition to the mature trees, but in hunted sites species with other dispersal modes dominated among seedlings. Seedlings emerging 1 year after clearing of all vegetation in experimental plots showed a similar pattern to the standing seedlings. This study thus verifies the transforming effects of bushmeat hunting on plant communities of tropical forests and is one of the first studies to do so for the African continent.

Sperm competition in tropical versus temperate zone birds.

Sperm competition represents an important component of post-copulatory sexual selection. It has been argued that the level of sperm competition declines in birds towards the equator. However, to date, sperm competition estimates have been available mainly for avian species inhabiting the northern temperate zone. Here we apply a novel approach, using the coefficient of between-male variation (CV(bm)) in sperm size as an index for sperm competition risk, in a comparative analysis of 31 Afrotropical and 99 northern temperate zone passerine species. We found no difference in sperm competition risk between the two groups, nor any relationship with migration distance. However, a multivariate model indicated that sperm competition risk was highest in species with a combination of low body mass and few eggs per clutch. The effect of clutch size was most pronounced in tropical species, which indicates that sperm competition risk in tropical and temperate species is differently associated with particular life-history traits. Although tropical species had lower sperm competition risk than temperate zone species for overlapping clutch sizes, the idea of a generally reduced risk of sperm competition in tropical birds was not supported by our analysis.

Genetic diversity of newcastle disease virus in wild birds and pigeons in West Africa.

In West and Central Africa, virulent Newcastle disease virus (NDV) strains of the recently identified genotypes XIV, XVII, and XVIII are enzootic in poultry, representing a considerable threat to the sector. The increasing number of reports of virulent strains in wild birds at least in other parts of the world raised the question of a potential role of wild birds in the spread of virulent NDV in sub-Saharan Africa as well. We investigated 1,723 asymptomatic birds sampled at live-bird markets and sites important for wild-bird conservation in Nigeria and 19 sick or dead wild birds in Côte d'Ivoire for NDV class I and II. Typical avirulent wild-type genotype I strains were found in wild waterfowl in wetlands in northeastern Nigeria. They were unrelated to vaccine strains, and the involvement of inter- or intracontinental migratory birds in their circulation in the region is suggested. Phylogenetic analyses also revealed that genotype VI strains found in pigeons, including some putative new subgenotype VIh and VIi strains, were introduced on multiple separate occasions in Nigeria. A single virulent genotype XVIII strain was found in a dead wild bird in Côte d'Ivoire, probably as a result of spillover from sick poultry. In conclusion, screening of wild birds and pigeons for NDV revealed the presence a variety of virulent and avirulent strains in West Africa but did not provide strong evidence that wild birds play an important role in the spread of virulent strains in the region.

Reassortant low-pathogenic avian influenza H5N2 viruses in African wild birds.

To investigate the presence and persistence of avian influenza virus in African birds, we monitored avian influenza in wild and domestic birds in two different regions in Nigeria. We found low-pathogenic avian influenza (LPAI) H5N2 viruses in three spur-winged geese (Plectropterus gambensis) in the Hadejia-Nguru wetlands. Phylogenetic analyses revealed that all of the genes, except the non-structural (NS) genes, of the LPAI H5N2 viruses were more closely related to genes recently found in wild and domestic birds in Europe. The NS genes formed a sister group to South African and Zambian NS genes. This suggested that the Nigerian LPAI H5N2 viruses found in wild birds were reassortants exhibiting an NS gene that circulated for at least 7 years in African birds and is part of the African influenza gene pool, and genes that were more recently introduced into Africa from Eurasia, most probably by intercontinental migratory birds. Interestingly the haemagglutinin and neuraminidase genes formed a sister branch to highly pathogenic avian influenza (HPAI) H5N2 strains found in the same wild bird species in the same wetland only 1 year earlier. However, they were not the closest known relatives of each other, suggesting that their presence in the wetland resulted from two separate introductions. The presence of LPAI H5N2 in wild birds in the Hadejia-Nguru wetlands, where wild birds and poultry occasionally mix, provides ample opportunity for infection across species boundaries, with the potential risk of generating HPAI viruses after extensive circulation in poultry.

Migration distance affects how closely Eurasian wigeons follow spring phenology during migration.

BACKGROUND: The timing of migration for herbivorous migratory birds is thought to coincide with spring phenology as emerging vegetation supplies them with the resources to fuel migration, and, in species with a capital breeding strategy also provides individuals with energy for use on the breeding grounds. Individuals with very long migration distances might however have to trade off between utilising optimal conditions en route and reaching the breeding grounds early, potentially leading to them overtaking spring on the way. Here, we investigate whether migration distance affects how closely individually tracked Eurasian wigeons follow spring phenology during spring migration. METHODS: We captured wigeons in the Netherlands and Lithuania and tracked them throughout spring migration to identify staging sites and timing of arrival. Using temperature-derived indicators of spring phenology, we investigated how maximum longitude reached and migration distance affected how closely wigeons followed spring. We further estimated the impact of tagging on wigeon migration by comparing spring migratory timing between tracked individuals and ring recovery data sets. RESULTS: Wigeons migrated to locations between 300 and 4000 km from the capture site, and migrated up to 1000 km in a single day. We found that wigeons migrating to more north-easterly locations followed spring phenology more closely, and increasingly so the greater distance they had covered during migration. Yet we also found that despite tags equalling only around 2% of individual's body mass, individuals were on average 11-12 days slower than ring-marked individuals from the same general population. DISCUSSION: Overall, our results suggest that migratory strategy can vary dependent on migration distance within species, and even within the same migratory corridor. Individual decisions thus depend not only on environmental cues, but potentially also trade-offs made during later life-history stages.

Evidence of infection by H5N2 highly pathogenic avian influenza viruses in healthy wild waterfowl.

The potential existence of a wild bird reservoir for highly pathogenic avian influenza (HPAI) has been recently questioned by the spread and the persisting circulation of H5N1 HPAI viruses, responsible for concurrent outbreaks in migratory and domestic birds over Asia, Europe, and Africa. During a large-scale surveillance programme over Eastern Europe, the Middle East, and Africa, we detected avian influenza viruses of H5N2 subtype with a highly pathogenic (HP) viral genotype in healthy birds of two wild waterfowl species sampled in Nigeria. We monitored the survival and regional movements of one of the infected birds through satellite telemetry, providing a rare evidence of a non-lethal natural infection by an HP viral genotype in wild birds. Phylogenetic analysis of the H5N2 viruses revealed close genetic relationships with H5 viruses of low pathogenicity circulating in Eurasian wild and domestic ducks. In addition, genetic analysis did not reveal known gallinaceous poultry adaptive mutations, suggesting that the emergence of HP strains could have taken place in either wild or domestic ducks or in non-gallinaceous species. The presence of coexisting but genetically distinguishable avian influenza viruses with an HP viral genotype in two cohabiting species of wild waterfowl, with evidence of non-lethal infection at least in one species and without evidence of prior extensive circulation of the virus in domestic poultry, suggest that some strains with a potential high pathogenicity for poultry could be maintained in a community of wild waterfowl.

Effects of season, water and predation risk on patch use by birds on the African savannah.

Birds from semi-arid regions may suffer dehydration during hot, dry seasons with low food availability. During this period, both energetic costs and water requirements for thermoregulation increase, limiting the scope of activity. For granivorous birds feeding on dry seeds, this is a major challenge and availability of water may affect the value of food. Water availability could (1) increase the value of a food patch when the surrounding environment is poor, due to an increase in the marginal value of energy, and (2) increase the value of the entire environment to the forager when environmental quality increases, due to an increase in the marginal value of time. We aimed to test this by measuring giving-up densities (GUDs, remaining food densities after foraging) of granivorous birds in the presence or absence of filled water pots, at different seasons differing in background food and water availability. We predicted that GUDs will increase with water provision during the dry season with moderate food, but in the early wet season with low food and water availability, GUDs will decrease with water provision. Later in the wet season, our experimental addition of water should have no effect. During seasons with low water availability but differing in food availability, results confirmed our predictions. However, when water became more abundant as the wet season progressed, birds still foraged more intensely during days with added water. In all seasons, birds fed more intensely in cover than in exposed areas, suggesting that predation risk rather than heat influenced microhabitat selection.

Sperm length variation among Afrotropical songbirds reflects phylogeny rather than adaptations to the tropical environment.

Sperm cells vary tremendously in size and shape across the animal kingdom. In songbirds (Aves: Passeri), sperm have a characteristic helical form but vary considerably in size. Most of our knowledge about sperm morphology in this group stems from studies of species in the Northern temperate zone, while little is known about the numerous species in the tropics. Here we examined sperm size in 125 Afrotropical songbird species with emphasis on the length of the major structural components (head, midpiece, flagellum), and total sperm length measured using light microscopy. Mean total sperm length varied from 51 µm to 212 µm across species. Those belonging to the Corvoidea superfamily had relatively short sperm with a small midpiece, while those of the three major Passeridan superfamilies Passeroidea, Muscicapoidea and Sylvioidea showed large interspecific variation in total sperm length and associated variation in midpiece length. These patterns are consistent with previous findings for temperate species in the same major clades. A comparative analysis with songbird species from the Northern temperate zone (N = 139) showed large overlap in sperm length ranges although certain temperate families (e.g. Parulidae, Emberizidae) typically have long sperm and certain Afrotropical families (e.g. Cisticolidae, Estrildidae) have relatively short sperm. Afrotropical and temperate species belonging to the same families showed no consistent contrasts in sperm length. Sperm length variation among Afrotropical and Northern temperate songbirds exhibits a strong phylogenetic signal with little or no evidence for any directional latitudinal effect among closely related taxa.

Competition, seed dispersal and hunting: what drives germination and seedling survival in an Afrotropical forest?

Disentangling the contributions of different processes that influence plant recruitment, such as competition and seed dispersal, is important given the increased human-mediated changes in tropical forest ecosystems. Previous studies have shown that seedling communities in an Afrotropical rainforest in southeastern Nigeria are strongly affected by the loss of important seed-dispersing primates, including Cross River gorillas (Gorilla gorilla diehli), chimpanzee (Pan troglodytes elioti) and drill (Mandrillus leucophaeus). Here we study how germination and survival of tree seedlings are affected by competition and reduced seed dispersal in three contiguous forest reserves, in southeastern Nigeria, with similar mature tree species composition and structure. We use an experimental design aimed at manipulating the effect of competition among seedlings in three protected and three hunted sites within the reserves. We use a total of sixty 5 × 5 m plots of three types: plots cleared of all seedlings, plots selectively cleared of all primate-dispersed seedlings and control plots. All seedlings were identified, measured, assigned to dispersal mode and tagged, and after 1 year we evaluated survival, mortality and new recruits. We found that in hunted sites germination of abiotically dispersed species was over four times higher in cleared plots compared to control plots, whereas germination of primate-dispersed species was the same, which indicated that dispersal limitation was the dominant force in seedling recruitment in hunted sites. This was supported by the fact that the germination of all dispersal modes in the selectively cleared plots in protected sites was similar to the control plots in the same sites, but germination of abiotically dispersed species was significantly lower than in cleared plots in hunted sites. Competition among seedlings was mostly evident from the fact that 75 % more seedlings of primate-dispersed species germinated in cleared compared to control plots in protected sites. We conclude that inter-seedling competition may be irrelevant to seedling recruitment in hunted sites, where dispersal limitation appears to be a much stronger force shaping the seedling plant community, and thus hunting indirectly reverses the importance of competition and dispersal limitation in structuring seedling communities.

Dramatic orientation shift of white-crowned sparrows displaced across longitudes in the high Arctic.

Advanced spatial-learning adaptations have been shown for migratory songbirds, but it is not well known how the simple genetic program encoding migratory distance and direction in young birds translates to a navigation mechanism used by adults. A number of convenient cues are available to define latitude on the basis of geomagnetic and celestial information, but very few are useful to defining longitude. To investigate the effects of displacements across longitudes on orientation, we recorded orientation of adult and juvenile migratory white-crowned sparrows, Zonotrichia leucophrys gambelii, after passive longitudinal displacements, by ship, of 266-2862 km across high-arctic North America. After eastward displacement to the magnetic North Pole and then across the 0 degrees declination line, adults and juveniles abruptly shifted their orientation from the migratory direction to a direction that would lead back to the breeding area or to the normal migratory route, suggesting that the birds began compensating for the displacement by using geomagnetic cues alone or together with solar cues. In contrast to predictions by a simple genetic migration program, our experiments suggest that both adults and juveniles possess a navigation system based on a combination of celestial and geomagnetic information, possibly declination, to correct for eastward longitudinal displacements.

Dual phylogenetic origins of Nigerian lions (Panthera leo).

Lion fecal DNA extracts from four individuals each from Yankari Game Reserve and Kainji-Lake National Park (central northeast and west Nigeria, respectively) were Sanger-sequenced for the mitochondrial cytochrome b gene. The sequences were aligned against 61 lion reference sequences from other parts of Africa and India. The sequence data were analyzed further for the construction of phylogenetic trees using the maximum-likelihood approach to depict phylogenetic patterns of distribution among sequences. Our results show that Nigerian lions grouped together with lions from West and Central Africa. At the smaller geographical scale, lions from Kainji-Lake National Park in western Nigeria grouped with lions from Benin (located west of Nigeria), whereas lions from Yankari Game Reserve in central northeastern Nigeria grouped with the lion populations in Cameroon (located east of Nigeria). The finding that the two remaining lion populations in Nigeria have different phylogenetic origins is an important aspect to consider in future decisions regarding management and conservation of rapidly shrinking lion populations in West Africa.

Individual identification and genetic variation of lions (Panthera leo) from two protected areas in Nigeria.

This survey was conducted in two protected areas in Nigeria to genetically identify individual lions and to determine the genetic variation within and between the populations. We used faecal sample DNA, a non-invasive alternative to the risky and laborious task of taking samples directly from the animals, often preceded by catching and immobilization. Data collection in Yankari Game Reserve (YGR) spanned through a period of five years (2008 -2012), whereas data in Kainji Lake National Park (KLNP) was gathered for a period of three years (2009, 2010 and 2012). We identified a minimum of eight individuals (2 males, 3 females, 3 unknown) from YGR and a minimum of ten individuals (7 males, 3 females) from KLNP. The two populations were found to be genetically distinct as shown by the relatively high fixation index (FST  = 0.17) with each population exhibiting signs of inbreeding (YGR FIS  = 0.49, KLNP FIS  = 0.38). The genetic differentiation between the Yankari and Kainji lions is assumed to result from large spatial geographic distance and physical barriers reducing gene flow between these two remaining wild lion populations in Nigeria. To mitigate the probable inbreeding depression in the lion populations within Nigeria it might be important to transfer lions between parks or reserves or to reintroduce lions from the zoos back to the wild.

Detecting shifts of transmission areas in avian blood parasites: a phylogenetic approach.

We investigated the degree of geographical shifts of transmission areas of vector-borne avian blood parasites (Plasmodium, Haemoproteus and Leucocytozoon) over ecological and evolutionary timescales. Of 259 different parasite lineages obtained from 5886 screened birds sampled in Europe and Africa, only two lineages were confirmed to have current transmission in resident bird species in both geographical areas. We used a phylogenetic approach to show that parasites belonging to the genera Haemoproteus and Leucocytozoon rarely change transmission area and that these parasites are restricted to one resident bird fauna over a long evolutionary time span and are not freely spread between the continents with the help of migratory birds. Lineages of the genus Plasmodium seem more freely spread between the continents. We suggest that such a reduced transmission barrier of Plasmodium parasites is caused by their higher tendency to infect migratory bird species, which might facilitate shifting of transmission area. Although vector-borne parasites of these genera apparently can shift between a tropical and a temperate transmission area and these areas are linked with an immense amount of annual bird migration, our data suggest that novel introductions of these parasites into resident bird faunas are rather rare evolutionary events.

Using stable isotopes to investigate migratory connectivity of the globally threatened aquatic warbler Acrocephalus paludicola.

Understanding the links between breeding and wintering areas of migratory species has important ecological and conservation implications. Recently, stable isotope technology has been used to further our understanding. Stable isotope ratios vary geographically with a range of biogeochemical factors and isotope profiles in organisms reflect those in their food and environment. For inert tissues like feathers, isotope profiles reflect the environment in which they were formed. Following large-scale habitat destruction, the globally threatened aquatic warbler Acrocephalus paludicola has a fragmented breeding population across central Europe, largely in Belarus, Poland and Ukraine. The species' sub-Saharan African wintering grounds have not yet been discovered, and this significantly hampers conservation efforts. Aquatic warblers grow their flight feathers on their wintering grounds, and we analysed stable isotope ratios (delta(15)N, delta(13)C, delta D) in rectrices of adults from six main breeding sites (subpopulations) across Europe to determine whether different breeding subpopulations formed a single mixed population on the wintering grounds. delta(15)N varies considerably with dietary trophic level and environmental factors, and delta D with the delta D in rainfall; neither varied between aquatic warbler subpopulations. Uniform feather delta(15)N signatures suggest no major variation in dietary trophic level during feather formation. High variance and inter-annual differences in mean delta D values hinder interpretation of these data. Significant differences in mean delta(13)C ratios existed between subpopulations. We discuss possible interpretations of this result, and consider differences in moulting latitude of different subpopulations to be the most parsimonious. delta(13)C in plants and animals decreases with latitude, along a steep gradient in sub-Saharan Africa. Birds from the most northwesterly breeding subpopulation (Karsibor, Poland) had significantly lower variance in delta(13)C and delta(15)N than birds from all other sites, suggesting either that birds from Karsibor are less geographically dispersed during moult, or moult in an area with less isotopic heterogeneity. Mean delta(13)C signatures from winter-grown feathers of different subpopulations were positively correlated with the latitude and longitude of breeding sites, suggesting a strong relationship between European breeding and African winter moulting latitudes. The use of stable isotopes provides novel insights into migratory connectivity and migration patterns in this little-known threatened species.