Assessment of microsatellite and SNP markers for parentage assignment in ex situ African Penguin (Spheniscus demersus) populations

Captive management of ex situ populations of endangered species is traditionally based on pedigree information derived from studbook data. However, molecular methods could provide a powerful set of complementary tools to verify studbook records and also contribute to improving the understanding of the genetic status of captive populations. Here, we compare the utility of single nucleotide polymorphisms (SNPs) and microsatellites (MS) and two analytical methods for assigning parentage in ten families of captive African penguins held in South African facilities. We found that SNPs performed better than microsatellites under both analytical frameworks, but a combination of all markers was most informative. A subset of combined SNP (n = 14) and MS loci (n = 10) provided robust assessments of parentage. Captive or supportive breeding programs will play an important role in future African penguin conservation efforts as a source of individuals for reintroduction. Cooperation among these captive facilities is essential to facilitate this process and improve management. This study provided us with a useful set of SNP and MS markers for parentage and relatedness testing among these captive populations. Further assessment of the utility of these markers over multiple (>3) generations and the incorporation of a larger variety of relationships among individuals (e.g., half‐siblings or cousins) is strongly suggested

Collapse of breeding success in desert-dwelling hornbills evident within a single decade

Rapid anthropogenic climate change potentially severely reduces avian breeding success. While the consequences of high temperatures and drought are reasonably well-studied within single breeding seasons, their impacts over decadal time scales are less clear. We assessed the effects of air temperature (Tair) and drought on the breeding output of southern yellow-billed hornbills (Tockus leucomelas; hornbills) in the Kalahari Desert over a decade (2008–2019). We aimed to document trends in breeding performance in an arid-zone bird during a time of rapid global warming and identify potential drivers of variation in breeding performance. The breeding output of our study population collapsed during the monitoring period. Comparing the first three seasons (2008–2011) of monitoring to the last three seasons (2016–2019), the mean percentage of nest boxes that were occupied declined from 52% to 12%, nest success from 58% to 17%, and mean fledglings produced per breeding attempt from 1.1 to 0.4. Breeding output was negatively correlated with increasing days on which Tmax (mean maximum daily Tair) exceeded the threshold Tair at which male hornbills show a 50% likelihood of engaging in heat dissipation behavior [i.e., panting (Tthresh; Tair = 34.5◦C)] and the occurrence of drought within the breeding season, as well as later dates for entry into the nest cavity (i.e., nest initiation) and fewer days post-hatch, spent incarcerated in the nest by the female parent. The apparent effects of high Tair were present even in non-drought years; of the 115 breeding attempts that were recorded, all 18 attempts that had ≥ 72% days during the attempt on which Tmax > Tthresh failed (equivalent to Tmax during the attempt ≥ 35.7◦C). This suggests that global warming was likely the primary driver of the recent, rapid breeding success collapse. Based on current warming trends, the Tmax threshold of 35.7◦C, above which no successful breeding attempts were recorded, will be exceeded during the entire hornbill breeding season by approximately 2027 at our study site. Therefore, our findings support the prediction that climate change may drive rapid declines and cause local extinctions despite the absence of direct lethal effects of extreme heat events.The DST-NRF Center of Excellence at the FitzPatrick Institute, Natural Environment Research Council, and the National Research Foundation of South Africa.http://frontiersin.org/Ecology_and_Evolutiondm2022Zoology and Entomolog

Rapid radiation of Southern Ocean shags in response to receding sea ice

Understanding how natural populations respond to climatic shifts is a fundamental goal of biological research in a fast-changing world. The Southern Ocean represents a fascinating system for assessing large-scale climate-driven biological change, as it contains extremely isolated island groups within a predominantly westerly, circumpolar wind and current system. Blue-eyed shags represent a paradoxical seabird radiation—a circumpolar distribution implies strong dispersal capacity yet their species-rich nature suggests local adaptation and isolation. Here we attempt to resolve this paradox in light of the history of repeated cycles of climate change in the Southern Ocean

Rapid loss of flight in the Aldabra white-throated rail

Flight loss has evolved independently in numerous island bird lineages worldwide, and particularly in rails (Rallidae). The Aldabra white-throated rail (Dryolimnas [cuvieri] aldabranus) is the last surviving flightless bird in the western Indian Ocean, and the only living flightless subspecies within Dryolimnas cuvieri, which is otherwise volant across its extant range. Such a difference in flight capacity among populations of a single species is unusual, and could be due to rapid evolution of flight loss, or greater evolutionary divergence than can readily be detected by traditional taxonomic approaches. Here we used genetic and morphological analyses to investigate evolutionary trajectories of living and extinct Dryolimnas cuvieri subspecies. Our data places D. [c.] aldabranus among the most rapid documented avian flight loss cases (within an estimated maximum of 80,000–130,000 years). However, the unusual intraspecific variability in flight capacity within D. cuvieri is best explained by levels of genetic divergence, which exceed those documented between other volant taxa versus flightless close relatives, all of which have full species status. Our results also support consideration of Dryolimnas [cuvieri] aldabranus as sufficiently evolutionary distinct from D. c. cuvieri to warrant management as an evolutionary significant unit. Trait variability among closely related lineages should be considered when assessing conservation status, particularly for traits known to influence vulnerability to extinction (e.g. flightlessness)

Genetic monitoring of ex-situ African Penguin (Spheniscus demersus) populations in South Africa

The African Penguin (Spheniscus demersus) has suffered population declines and is listed in the IUCN Red List as Endangered. The species is endemic to the coast of southern Africa, and breeding colonies are distributed on the south-western coast of Africa. Currently, African Penguins are being kept in zoo and aquarium facilities throughout South Africa. In this study, molecular genetic data based on 12 microsatellite markers from 1 119 African Penguin samples from four facilities were generated in order to determine the level of genetic variation, population structure and differentiation, and effective population size to assist in the development of an effective captive management plan. Expected heterozygosity ranged from 0.57 to 0.62, and allelic richness from 4.2 to 5.1. However, based on differences between first- and second-generation captive birds, we conclude that the ex situ population is at risk of losing genetic variability in the future and management programmes should include exchange of birds between captive facilities in order to induce gene flow and increase effective population size. Adding individuals from in situ populations should also be considered in the future in cases where these birds cannot be rehabilitated. Molecular genetic analyses of wild penguin populations should be carried out for comparison, and to ascertain to what degree ‘in situ genetic diversity’ is represented among ex situ populations. With regular resampling and analyses, the extent of the effect of processes such as genetic drift on diversity in the ex situ penguin populations will become evident.Keywords: African Penguin, microsatellite, monitoring, Spheniscus demersu

Genetic monitoring of ex situ African Penguin (Spheniscus demersus) populations in South Africa

The African Penguin (Spheniscus demersus) has suffered population declines and is listed in the IUCN Red List as Endangered. The species is endemic to the coast of southern Africa, and breeding colonies are distributed on the south-western coast of Africa. Currently, African Penguins are being kept in zoo and aquarium facilities throughout South Africa. In this study, molecular genetic data based on 12 microsatellite markers from 1 119 African Penguin samples from four facilities were generated in order to determine the level of genetic variation, population structure and differentiation, and effective population size to assist in the development of an effective captive management plan. Expected heterozygosity ranged from 0.57 to 0.62, and allelic richness from 4.2 to 5.1. However, based on differences between first- and second-generation captive birds, we conclude that the ex situ population is at risk of losing genetic variability in the future and management programmes should include exchange of birds between captive facilities in order to induce gene flow and increase effective population size. Adding individuals from in situ populations should also be considered in the future in cases where these birds cannot be rehabilitated. Molecular genetic analyses of wild penguin populations should be carried out for comparison, and to ascertain to what degree ‘in situ genetic diversity’ is represented among ex situ populations. With regular resampling and analyses, the extent of the effect of processes such as genetic drift on diversity in the ex situ penguin populations will become evident.Keywords: African Penguin, microsatellite, monitoring, Spheniscus demersu

Correction: Rapid loss of flight in the Aldabra white-throated rail.

[This corrects the article DOI: 10.1371/journal.pone.0226064.]

Assessment of genetic and morphological differentiation among populations of the Diederik Cuckoo <i>Chrysococcyx caprius</i>

The Diederik Cuckoo Chrysococcyx caprius is an African species widely distributed south of the Sahara, which migrates seasonally between breeding and nonbreeding sites. It is currently unknown whether the species consists of a single panmictic population or if it is genetically structured. To investigate this, we analysed sequence variation in three mitochondrial and two nuclear gene regions in combination with morphological measurements in specimens from four localities. Phylogenetic relationships were estimated using maximum-likelihood methods and included samples of Klaas’s Cuckoo Chrysococcyx klaas, Red-chested Cuckoo Cuculus solitarius, and African Cuckoo Cuculus gularis. Haplotype networks and analysis of molecular variance were used to characterise the spatial distribution of genetic diversity. A principal component analysis was performed to investigate morphological variation among localities. Molecular analysis identified two divergent mitochondrial lineages, which were found to occur in sympatry in one South African locality (Limpopo Province). The magnitude of divergence between versus within these lineages was low (0.4–1%) yet significant (FST: 0.84–0.88). Lack of apparent phylogeographic structure provides support for the absence of physical barriers to gene flow in this species. The divergent mitochondrial lineages did not differ in morphological measurements. The emergence and persistence of shallow mitochondrial divergence among sympatric lineages in the Diederik Cuckoo could be linked to maternal divergence in host selection of these brood parasites — a hypothesis requiring additional data to be tested.</p