Research Article |
Corresponding author: Guinevere O. U. Wogan ( gwogan@okstate.edu ) Academic editor: Robert Whittaker
© 2024 Guinevere O. U. Wogan, Gary Voelker, Tanya Jain, Potiphar Kaliba, Rauri C. K. Bowie.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Wogan GOU, Voelker G, Jain T, Kaliba P, Bowie RCK (2024) Niche dynamics modulate population connectivity between disjunct ranges of the Cape Robin-chat (Cossypha caffra) supporting an aridlands species pump. Frontiers of Biogeography 17: e132679. https://doi.org/10.21425/fob.17.132679
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Southern Africa boasts an extraordinary diversity of birds, posited to have at least in part been driven by a “species pump” model, facilitated by an intermittent arid corridor connecting it with northeast Africa. This arid corridor arose and disappeared in concert with Plio-Pleistocene climate fluctuations, providing a means for northern, primarily arid-adapted lineages, to disperse to and subsequently colonize Southern Africa. Here, we test this “species pump” at the intra-specific level. We focus on Cape Robin-chats (Cossypha caffra) which have disjunct resident populations in the forested mountains of East Africa and in the aridlands of Southern Africa. We use multi-locus data to estimate gene flow between these populations, model spatial connectivity across this region contemporaneously and over the past 120 thousand years, and test niche differentiation. We found evidence for highly asymmetric gene flow (north to south) among Cape Robin-chat populations, and niche differentiation coupled with an inferred niche-based environmental filter limiting gene flow from southern to northern populations. Habitat suitability supports the presence of an intermittent corridor stretching from the Horn of Africa to Southern Africa. We propose that a modified species pump incorporating niche divergence and subsequent dispersal limitation driven by environmental filters has contributed to population differentiation among northern and southern populations of Cape Robin-chats, and that this same mechanism over time may have contributed to the rich avifaunal diversity of Southern Africa.
Southern Africa has rich avifauna with high endemicity driven in part by in situ speciation.
Using a combination of genetic analyses, niche models, and dispersal models, we find support for an intermittent aridlands corridor between disjunct populations of Cape Robin-chats modulated by Plio-Pleistocene climatic oscillations.
This study shows niche divergence and asymmetric gene flow between southern and northern populations, providing a mechanism for population divergence.
This supports the existence of an aridlands species pump that drives population divergence and may have contributed to species diversification in the Southern Africa avifauna.
Africa, aridlands, biogeography, birds, disjunct range, niche overlap, population connectivity
Latitudinal and elevational gradients are known to structure diversity across most terrestrial realms (
Across Africa, these gradients play out across a highly dynamic landscape that has seen vast contraction and reorganization of forest habitats, and expansion of aridlands, dating to the Miocene (
However, not all African bird species fit into the neat categorization of “aridland” or “forest” adapted species. The polytypic Cape Robin-Chat (Cossypha caffra) is widely distributed across the aridlands of southern Africa, and recent work has demonstrated that there are three genetic clusters in southern Africa that correspond with several Pleistocene aridland habitat refugia (
The diversity of habitats occupied in the northern and southern portions of the range, and the associated latitudinal gradient suggest that the northern and southern populations of C. caffra may be locally adapted to divergent environments. The shift to a new habitat may or may not be accompanied by an associated shift in the climatic niche of C. caffra. Since temperature, latitude and elevation are all tightly linked, for example with higher temperatures at both lower latitudes and lower elevations, from first principles we can expect that temperatures on tropical mountains and temperatures at high latitudes have the potential to be equivalent. For example, we know that a 100 meter increase in elevation causes a temperature decrease of up to ~1°C, and is roughly equivalent to a latitudinal movement of ~197 km of distance in the southern hemisphere, since with each degree of increasing southern latitude, temperature decreases 0.5°C (
We hypothesize that the Plio-Pleistocene climatic oscillations created temporally dynamic corridors and barriers to population connectivity between the Horn of Africa and southern Africa. These dynamic corridors and barriers are respectively regions of high or low environmental suitability determined in part by the species niche. Niche dynamics are modulated by the extent of gene flow between populations since gene flow can either disrupt local adaptation by homogenizing the gene pool, or promote adaptation by increasing genetic variation and introducing advantageous alleles (
To determine the extent to which fluctuating corridors and niche dynamics may have played a role in structuring C. caffra populations, we estimate contemporary and historical population connectivity using a combination of environmental niche models and multi-locus genetic data. If population connectivity is low, gene flow between northern and southern populations will be reduced to absent and this would translate to substantial population structure and rare instances of admixed individuals with north and south parentage. Conversely, if population connectivity is high, gene flow will be extensive between northern and southern populations, which would result in little population substructure between northern and southern populations, and a high proportion of individuals with admixed parentage.
We also assess evidence for climatic niche conservatism or niche divergence accompanying the shift in habitat usage between the northern and southern populations of C. caffra. If the climatic niche is conserved this would suggest the observed habitat differences between the northern and southern populations are underscored by maintenance of a specific climatic niche via climatic niche tracking. We expect to find substantial niche overlap between northern and southern populations if the niche is conserved. Alternatively, under a scenario of niche divergence we can infer that the climatic niche has shifted. The shift may be in one or both populations, and it may be adaptive or plastic, either driven by local adaptation or by the availability of realized niche space. With niche divergence we expect to find little or no evidence of niche overlap.
Through the assessment of niche dynamics and gene flow across this region at the population-level for a single species, we are able to test the mechanism by which the species pump has acted to generate avian species diversity.
We obtained occurrence data for Cossypha caffra from throughout their distribution from GBIF and limited our search to vouchered specimens (
Total genomic DNA was extracted using a Quiagen DnEasy kit according to manufacturer protocols. Building on a previous dataset (
For each subspecies we calculated the number of private alleles, expected and observed heterozygosity, allelic richness, and theta (an FST estimator), and then evaluated evidence for population differentiation between them. For population differentiation tests, we calculated FST, Joost’s D, Χ2, and GST measures with 1000 replicates to estimate overall and pairwise differentiation. All of these analyses were carried out in the R package StrataG (
To evaluate if there is evidence of admixture between the northern and southern resident populations, we used an admixture model, testing k values from 2 to 6 with 20 replicates at each k, with a burnin of 10,000 steps and 100,000 steps post burnin in Structure (
We assessed the ancestry of each individual by statistically assigning them to an ancestry class (parental southern, parental northern, F1, F2+, backcross) to better understand the nature of admixture in this species. We used the Bayesian assignment method implemented in NewHybrids v. 1.1 (
To capture estimates of gene flow between the northern and southern populations of Cossypha caffra, we used a coalescent approach as implemented in migrate-n (
We used graph theory to estimate genetic connectivity among populations. We used the conditional genetic distance statistic (cGD) (
We generated environmental niche models (ENMs) for Cossypha caffra. We projected ENMs onto paleoclimate reconstructions to assess the suitability of climate for the two delineated genetic clusters corresponding to north and south in a spatially explicit framework. We generated ENMs for the present using MaxEnt v. 3.4.1 (
To assess movement through time, we used an explicit dispersal model to generate maps of accessibility given a northern versus a southern origin of Cape Robin using the KISSmig R package (
Using the GBIF data in combination with records from our work, we assessed niche breadth using two measures, B1 and B2 (
Our sampling consisted of 335 individuals including representatives of all currently recognized Cossypha caffra subspecies: C. caffra caffra, C. c. iolaema, C. c. kivuensis, and C. c. namaquensis (Fig.
Geographic range of Cossypha caffra, by subspecies: Cossypha caffra caffra (green), Cossypha caffra iolaema (blue), Cossypha caffra kivuensis (orange), Cossypha caffra namaquensis (purple). In each colored-shaded area, the darker colored shape(s) reflect Cossypha caffra ranges denoted in Birdlife International, while the lighter colored shape is an expanded area to encompass samples from outside Birdlife’s depiction of range. Within the expanded area, lighter circles are the sampling localities for which we generated genetic data, and darker circles are vouchered localities used for building ENMs obtained from our fieldwork and GBIF. Cape Robin-Chat by JMK - Own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=40318949.
The number of alleles for each locus ranged from 10 to 35, and allelic richness ranged from 0.03 to 0.14 (Suppl. material
Using the defined subspecies as our pre-defined populations, we found that permutation tests provided evidence for population differentiation among the subspecies using Joost’s D (0.2056, p-value: 0.0009) and ChiSq (3118.6682, p-value: 0.0009) metrics. Pairwise comparisons supported this finding for all subspecies (Suppl. material
The population analyses identified a best-fit of three clusters within the dataset (Fig.
Results from population structure analyses for Cossypha caffra depicting the clustering recovered for k-values of 2 to 4. The analyses recovered a best fit of three clusters in the data. These correspond with two clusters in southern Africa (South Africa, Namibia, Mozambique) and one encompassing all of the northern populations (Malawi, Tanzania, Democratic Republic of Congo).
We recovered a signal suggesting that there is admixture between the northern and southern regions, with ancestry proportions for two individuals representing both southern clusters amidst the northern populations, and northern ancestry identified among the southern African populations (Fig.
Most individuals were assigned to an ancestry category with high certainty (> .80). The results assigned 247 samples as southern parentals, 27 samples assigned as northern parentals, and 15 samples were assigned as F2s. No individuals were assessed to be F1s or back-crosses. C. caffra caffra and C. caffra namaquensis individuals were assigned as southern parentals or F2s. C. caffra iolaema samples were assigned as northern parentals or F2s, and of the three C. caffra kivuensis samples, one was assigned with certainty as an F2, while the others were assigned with ambiguity as either a northern parental or an F2. When probabilities for each of the ancestry categories are plotted with respect to geography, the assignments suggest that there is a distinctive divide between northern and southern assignment near the Mozambique – Tanzania border (Fig.
Spatial Genetic Connectivity of Cossypha caffra populations. Panel A ScatterPie charts depicting the geographic distribution of ancestry categories. The red bar at the Mozambique-Tanzania border depicts the divide between the northern and southern lineages. Black arrows depict the intensity of gene flow between northern and southern lineages. Panel B (top) depicts a population graph in which nodes are sampling localities and edges represent gene flow, the nodes are scaled by sample size. Panel B (bottom) shows the network within geographical context.
The estimates of gene flow between the northern and southern populations of C. caffra suggest highly asymmetric patterns of gene flow between the northern and southern populations, with northern gene flow into southern populations at ten-fold greater levels than vice-versa (N to S 0.199, S to N 0.013) (Fig.
We recovered 13 stable edges (Suppl. material
We combined occurrence points from our sampling with vouchered occurrence points from GBIF for a total of 794 occurrences. These points are distributed throughout the range of Cossypha caffra (Fig.
The dispersal models, which are integrated across the past 120 thousand years were similar for both the Northern and the Southern Origin hypotheses, revealing that there are two connected areas, one consisting of South Africa, southern Namibia, Zimbabwe and Mozambique and another comprising a northern connected region encompassing the Democratic Republic of Congo, Malawi, Kenya, and Tanzania (Fig.
Integrated estimates of dispersal between disjunct populations of Cossypha caffra. These are migration surfaces integrated over the past 120 thousand years with either a northern (top) or southern (bottom) origin. The colors reflect the proportion of iterations in which there is an occurrence dark green (highest proportion of occurrence across iterations) to pink (rare occurrence) to white (no occurrence).
ENMs generated for the northern and southern populations independently revealed that for the northern populations, there is a corridor of environmental suitability between eastern Africa and southern Africa leading to the southern populations (Fig.
The symmetric background tests, both those based on ENMs and those based on environmental space, are also statistically significant for measures of Schoener’s D and Hellinger’s I (p-value of 0.01). The Spearman rank correlation has conflicting support, with the ENM- based measure not statistically significant (0.069), and the direct environment-based measure statistically significant (p-value of 0.01) (Suppl. material
Maps depicting the climatic suitability of the northern and southern populations of Cossypha caffra. Colors scale from light yellow (highly suitable) to black (not suitable). The points are the training (green) and testing (white) sampling points used for estimating environmental suitability.
Niche divergence. Panel A. The result of tests of Identity for Schoener’s D and modified Hellinger’s I statistics. The left three plots are generated from ENMs, while the right three plots are in environmental space. The dashed lines represent the observed value compared against a histogram that is the distribution generated through a resampling scheme. Panel B. Quantification of niche identity and background tests in environmental space, where the axes (x,y) represent the first two Principal Components of environmental space.
The disjunct resident populations of Cossypha caffra are distributed across a large latitudinal and elevational gradient. Within C. caffra, genetic diversity is structured with distinct northern and southern populations, and with the primary genetic break delineating populations located in eastern Africa near the Mozambique – Tanzania border. The rates of gene flow are highly asymmetric, with a ten-fold higher difference in north to south versus south to north estimates of gene flow. Genetic connectivity indicates that most of the north-south gene flow occurs from northern populations into the southern populations distributed across central and eastern South Africa, those inhabiting grassland and savanna habitats.
Other species have similar genetic breaks in eastern Africa (
Recent work has demonstrated that highly dynamic paleoclimatic perturbations arising from complex El Niño Southern Ocean oscillation (ENSO) have been linked to mammalian dispersal routes and corridors throughout Sub-Saharan Africa (
These findings are congruent with the hypothesized species pump paradigm as a species-generating force contributing to the high levels of avian species diversity in southern Africa, although under a modified scenario. Under this paradigm, the “species pump” for C. caffra involved the dispersal of the northern population individuals along the north-south corridor, resulting in the establishment of the southern populations. Given the lack of northward dispersal we would, under our modified species pump hypothesis, suggest that the southern populations have over time diverged and experienced niche evolution, giving rise to the locally adapted aridland populations that characterize the southern African populations of C. caffra.
All of our niche-based analyses support a scenario by which the northern and southern populations of C. caffra have divergent climatic niches, despite the overall similarity of the background environments between the northern and southern regions. This suggests that these populations either occupy different parts of their fundamental niches, or they have become locally adapted. To more fully explore the idea that these species are locally adapted, physiological assays and assessments of phenotypic differentiation would be required. Additionally, the use of genomic data to discern whether there are loci that exhibit differential associations with environmental gradient elements would potentially provide powerful insights into the eco-evolutionary dynamics at play in C. caffra diversification.
If the species pump paradigm has been acting as we hypothesize, then we would expect that multiple species of birds with similar geographically broad and environmentally diverse ranges will share the pattern recovered for C. caffra. Based on very limited evidence that southern to northern colonizations have occurred in African bird lineages (
In addition to the ecological divergence recovered for C. caffra in this study, others have suggested that shifts in habitat preference may be driven by biotic interaction with congeners, specifically C. heuglini (
We thank Martim Melo, anonymous reviewers, and FOB editorial team for their comments and insights. We are grateful to the provincial authorities in the Northern Cape, Western Cape, Eastern Cape, Limpopo, Kwazulu‐Natal, and Free State provinces of South Africa for granting permission to collect samples or specimens. GV thanks Beryl Wilson for subpermitting him via the McGregor Museum. Corne Anderson, Tom Gnoske, Penn Lloyd, Angela Ribeiro, and Dawie de Swardt are thanked for their valuable assistance in the field in South Africa, along with numerous landowners for allowing us to work on their property. We also thank permitting agencies in Malawi (National Commission for Science and Technology), Tanzania (Tanzania Commission for Science and Technology), Kenya (National Commission for Science, Technology, and Innovation), and Democratic Republic of Congo. This work was supported by NSF DEB‐0613668 and by collaborative grants NSF DEB‐1120356 and NSF DEB‐1119931 to G. Voelker and R. C. K. Bowie. This is publication number 1685 of the Biodiversity Research and Teaching Collections at Texas A&M University.
Designed the study: GOUW, RCKB, GV, Collected samples: RCKB, GV, PK, Generated Data: GOUW, Analyzed Data: GOUW, TJ, Wrote the manuscript: GOUW, RCKB, GV, Edited and approved the manuscript: GOUW, TJ, PK, RCKB, GV Obtained Funding to support the research: RCKB, GV.
Data in this paper are available in the Suppl. material
Supplementary tables (tables S1–S3) and figures (figs S1–S3) (.pdf)