Influence of historical and contemporary habitat changes on the population genetics of the endemic South African parrotPoicephalus robustus

Abstract

SummaryThe Cape Parrot Poicephalus robustus is a habitat specialist, restricted to forest patches in the Eastern Cape (EC), KwaZulu-Natal (KZN) and Limpopo provinces of South Africa. Recent census estimates suggest that there are less than 1,600 parrots left in the wild, although historical data suggest that the species was once more numerous. Fragmentation of the forest biome is strongly linked to climate change and exploitation of the forest by the timber industry. We examine the subpopulation structure and connectivity between fragmented populations across the distribution of the species. Differences in historical and contemporary genetic structure of Cape Parrots is examined by including both modern samples, collected from 1951 to 2014, and historical samples, collected from 1870 to 1946. A total of 114 individuals (historical = 29; contemporary = 85) were genotyped using 16 microsatellite loci. We tested for evidence of partitioning of genotypes at both a temporal and spatial scales by comparing shifts in allelic frequencies of historical (1870–1946) and contemporary (1951–2014) samples across the distribution of the species. Tests for population bottlenecks were also conducted to determine if anthropogenic causes are the main driver of population decline in this species. Analyses identified three geographically correlated genetic clusters. A southern group restricted to forest patches in the EC, a central group including birds from KZN and a genetically distinct northern Limpopo cluster. Results suggest that Cape Parrots have experienced at least two population bottlenecks. An ancient decline during the mid-Holocene (∼ 1,800-3,000 years before present) linked to climate change, and a more recent bottleneck, associated with logging of forests during the early 1900s. This study highlights the effects of climate change and human activities on an endangered species associated with the naturally fragmented forests of eastern South Africa. These results will aid conservation authorities with the planning and implementation of future conservation initiatives. In particular, this study emphasises the Eastern Cape mistbelt forests as an important source population for the species and calls for stronger conservation of forest patches in South Africa to promote connectivity of forest taxa.

Climate refugia for three Afromontane forest‐dependent bird species in south‐eastern South Africa

“…Although climatic suitability for these species was diminished at higher elevations during the LGM (Figure 4g–i), pockets of climatic refugia may have persisted along the Transkei Escarpment (Baziya) and Amatole Mountains (Kubusi and Fort Fordyce). Observed genetic diversity unique to these forests (Table S2; Figure 2b–d) suggests that these birds may have been present in such mid‐elevational areas during the LGM, corroborating genetic diversity trends within regional Afromontane forests (Velvet worms: Daniels et al, 2017; Barnes & Daniels, 2019; birds: Coetzer et al, 2020; Mulvaney et al, 2021; frogs: Kushata et al, 2020; monkeys: Madisha et al, 2018; chameleons: da Silva & Tolley, 2017).…”

“…Long‐term demographic decline within P. ruficapilla (Figure 2f; Table S6) suggests that these warblers were sensitive to climate‐induced forest subsidence from 1.0 to 3.6 kya (Lodder et al, 2018)—as observed within the South African endemic Cape parrot Poicephalus robustus (Coetzer et al, 2020)—which was potentially exacerbated by the arrival of Iron Age farmers into South Africa 1.2 kya (Neumann et al, 2014). Long‐term demographic declines can mask the detection of more recent population declines (Cornuet & Luikart, 1996), and so regional P. ruficapilla populations may be more sensitive to contemporary anthropogenic forest exploitation than currently understood (Mulvaney et al, 2021).…”

Species–landscape interactions drive divergent population trajectories in four forest‐dependent Afromontane forest songbird species within a biodiversity hotspot in South Africa

“…Runs were performed under both single‐step mutation model (SMM), and 10% single‐step two‐phase mutation (TPM) to accommodate a broader range of mutation dynamics within natural populations. Mutation models assumed a mutation rate of μ = 5 × 10 −4 per generation (Brohede et al, 2002 ; Coetzer et al, 2020 ), with an acceptance ratio of 0.25.…”

The impact of timber harvesting on nest site availability for the Cape Parrot Poicephalus robustus in native Southern Mistbelt forests of the Eastern Cape, South Africa

“…Key drivers of this have been habitat loss and degradation and associated losses of suitable nest sites, largely attributed to the extensive harvesting of yellowwoods that occurred between the late 19 th century and 1939 (Wirminghaus et al 1999(Wirminghaus et al , 2001. The southernmost population in the Amathole region in the Eastern Cape is the largest (Downs et al 2019), and an important source population (Coetzer et al 2019). It is thus essential that forests in this region are managed with consideration for Cape Parrot habitat requirements, particularly during critical life-history stages such as breeding.…”

“…They are the only endemic parrot species in South Africa, recognised globally as ‘Vulnerable’ given their small population size, currently estimated to be between 1,100–1,800 individuals (BirdLife International 2021). Its breeding habitat is restricted to montane mistbelt evergreen forests in the Eastern Cape and KwaZulu-Natal provinces, with a small, relict population in the northern province of Limpopo (Coetzer et al 2019). While their historic range was much more extensive (Clancey 1964), range and population declines have occurred over the last century (Wirminghaus et al 1999, Cooper et al 2017).…”