Thesis (M. Sc. (Zoology)) -- University of Limpopo, 2021 / The larks (Passeriformes, Passeri, Alaudidae) are small to medium-sized (10-23 cm) birds that are primarily terrestrial and cryptically plumaged hence they are difficult to encounter and recognise. The current taxonomic circumscription places these birds in a group that is comprised of 21 genera and 98 species, with all the genera occurring in Africa, 13 in Eurasia, and a single genus occurs in Australia and the Americas. Up until Alström et al. (2013), morphologically, the lark family was distinguished by having two unique and primitive features: i) the tarsus morphology (latiplantar and scutellate) consisting of the flat posterior surface covered with prominent scales, instead of being narrow and smooth as in other families, and ii) the syrinx (voice-generating organ). Despite that the structure of the syrinx of larks has been studied, literature reveals confusion pertaining to either the presence or absence of the pessulus, its level of development and size. To date, the work in Alström et al. (2013) remains the most comprehensive multi-locus phylogeny of the larks in which three strongly supported major clades (clade A – hereafter the Alaudid, clade B – the Mirafrid, clade C – the Ammomanid) emerged though with some uncertainty in some parts of the tree. In this study, the aim was to investigate the utility of syringeal and vocal characters in classifying the species of larks, finding out how syringeal and vocal characters evolved and identifying characters that define clades. The gross morphology and histology of the syringes and song strophes of larks and their putative outgroups were studied. Gross morphologically and histologically, the larks were found to possess a typical syrinx classified as a ‘syrinx tracheo-bronchialis’ and pessulus was observed in larks and the outgroups studied. There were differences observed in the syringeal gross morphological structure across all the three major clades (A, B and C). This is with regard to the presence or absence of the divided or double bronchial rings variably observed in clade A, B and C. In clade B and C, the ossification is variably restricted to the centre of bronchial rings forming a serial pattern while in clade A, bronchial rings are variably almost fully ossified without forming any serial pattern. The prominent oblique muscle-like structure runs ventrally and it was only observed in clade C in Chersomanes albofasciata. On the other hand, the syringeal histology revealed differences in the shape of the pessulus (blunt, pointy or sharp), the pessulus position relative to bronchial rings 1, 2 and 3 (B1, B2 and B3 respectively), length of the internal tympaniform membranes and connective tissue along the internal tympaniform membrane. The position of the pessulus was variably found to align with B2, to be below B2 and to be positioned beyond B2. One-way Anova clearly showed that among the three clades (A, B and C) identified in Alström et al. (2013), a statistically highly significant difference (P < 0.01) was found between the song strophes of species in clade C and A. The species in clade A generally give song strophes defined by high maximum frequency, high peak frequency and broad bandwidth frequency. The species in clade B have a similar trend with those in clade A, possibly explaining the overlap between these clades and the statistically significantly difference between clade A and C. These findings may be in support of the phylogenetic findings in Alström et al. (2013) and this study wherein clade A and B shared a sister relationship while clade C was placed basally. Clade C, on the other hand, comprises song strophes that are defined by low maximum frequency, lower peak frequency and narrow bandwidth frequency and this clade differed significantly from clade A. Despite that not all of the species could be correctly classified to their respective clades based on the Discriminant Function Analysis’ partition plot, the largest number of correct classifications were for clade A (70%). In addition, the distinction among the clades was also observed in either the presence or the absence of wing clappings in the song strophes, either being detached from or attached to the song strophes. Clade B is the only one which was marked by the presence of wing clappings particularly, genus Mirafra, although they are reported in Chersophilus duponti which belongs to clade A but not included in this study. With regard to the vocal phylogeny, the topology was highly unresolved, and no relationships could be inferred. The tracing of the evolution of characters of eight vocal and five syringeal characters revealed that among the 13 characters for which the ancestral state reconstructions were performed, 12 are polymorphic that is, they underwent multiple state changes ranging from four to 18. Most character states were found to plesiomorphous and mainly leading to clades of which their ancestral nodes were defined largely by autapormorphic and symplesiomorphic states. These do not assist in explaining how the various characters evolved. In conclusion, the findings have shed some light concerning the general syringeal morphology and histological structures of larks, revealed that lark songs are not suitable for reconstructing the phylogeny, shed light on the evolution of the selected vocal and syringeal characters as well as identifying characters that define the three major clades of larks (the Alaudid, Mirafrid and the Ammomanid).

Thesis (M.Sc. (Zoology)) -- University of Limpopo, 2012 / Sparrow-larks form a relatively small genus in the family Alaudidae and comprise only seven species distributed widely throughout Africa and parts of the Eurasian landmass. Sparrow-larks are unique amongst larks in that they are sexually dichromatic and exhibit biparental care. The chestnut-backed sparrow-lark Eremopterix leucotis is endemic to Africa with five subspecies recognized based on differences in plumage colouration. The five subspecies are distributed throughout the arid to semi-arid savannas of Africa with two subspecies (E. l. hoeschi and E. l. smithi) occurring in southern Africa. Despite their widespread occurrence and its interest for research on the evolution of characteristics in the family (e.g. being sexually dichromatic and exhibiting biparental care), very little is known of the biology and ecology of the Eremopterix larks. The chestnut-backed sparrow-lark is no exception and most of what we know of the species is based on incidental observations from a few nests. In an attempt to improve our knowledge of this interesting group of species, it was decided to study various aspects of the breeding biology and ecology, moult, vocalizations and geographical variation in the chestnutbacked sparrow-lark. The breeding biology of the chestnut-backed sparrow-lark was studied at Al3 farm (De Loskop) near Mogwadi in the Limpopo Province of South Africa from January 2008 to December 2010. Data collected during the study included: breeding seasonality, egg and clutch characteristics, duration of the incubation and nestling periods, nest-site characteristics, the roles and relative contribution of the sexes in the breeding cycle, nestling development, diet and nestling provisioning rate, and breeding success. Chestnut-backed sparrow-larks bred mostly during the dry season, which is from April to September in the study area. Nevertheless, the results revealed that breeding is bimodal with a main peak in breeding activity in late summer and autumn (March to April) and a second smaller peak in spring (September to October). The species showed geographical variation in clutch size with a mean of 1.88 eggs recorded in the study area as opposed to 1.00 recorded in the northern parts of its range. Egg dimensions compared well with measurements obtained from the Nest Record Card Scheme of the Animal Demography Unit, University of Cape Town, South Africa. The mean incubation period of 10.33 days recorded in this study compares favourably with that of other Eremopterix species viii (8–10 days), a genus with some of the shortest incubation periods amongst larks. The mean nestling period of 9.2 days (range: 8–10) in the study area was significantly less than the 10–12 days reported for populations in the northern range of the species, but it compares well with those of other sparrow-larks. Nest site characteristics, which were quantified within a 1 m2 quadrant with the nest as the centre, including nest dimensions, were consistent with those reported in the literature. Chestnut-backed sparrow-larks in the study area preferred to nest in areas with a high percentage of bare ground (median = 67.5%) and very little vegetation cover (median = 25%). Most nests faced in a southerly direction compared to nests in the north of the species’ range, which face in a north-easterly or easterly direction. The species’ preference to face the nests away from the midday sun most probably serves a thermoregulatory function to avoid excessive heat during the warmest parts of the day. Most nests (78.2%) had an apron varying in size from small and insignificant to large and well-developed. The functional significance of the apron remains a matter of conjecture and there was no association between breeding success and presence or absence of the apron. In addition, one pair constructed one nest with and another without an apron, suggesting that individual preference or characteristic is not a determinant factor in the construction of an apron. Both sexes took part in nest construction, incubation and feeding and brooding of nestlings. However, the relative contributions were not entirely symmetrical as males incubated a greater proportion (50.1%) of the time compared to females (43.1%), and the mean and median of male incubation shift lengths were longer than that of females, albeit not statistically significant. However, females made statistically significantly (P < 0.05) more nest visits to deliver food compared to males (54.6% vs. 45.5%). The average breeding success, estimated using Mayfield’s method, was 16.1% but there were inter-annual differences with the overall breeding success in 2010 being only 8.1% compared to 20.6% of 2008. Known causes of failure included nest depredation, flooding, starvation, nest abandonment and hatching failure. Statistical analysis of morphometric data of live specimens and museum study skins suggest that, in addition to being sexually dichromatic, chestnut-backed sparrowlarks also exhibit mild sexual size dimorphism. However, there was considerable overlap in these measurements between the sexes and as a result the biological significance of this sexual size dimorphism may be negligible. Nevertheless, the ix results show chestnut-backed sparrow-lark males tend to have longer wings and tails compared to females. This may be adaptive with respect to the extended display flights that males perform during the breeding season. Interestingly, the mean mass of breeding females in the study area was significantly more compared to males, whereas the SAFRING database, representing data recorded throughout the year, showed no significant differences in the mean mass between the sexes. The greater mass of breeding females may relate to physiological changes associated with the acquisition of resources and the development of structures and tissues associated with egg-laying and egg-production. Larks rely heavily on vocalizations to attract mates and advertise territories. Not surprisingly, the study revealed a rich vocal repertoire for the chestnut-backed sparrow-lark. The analysis of the vocalizations shows that chestnut-backed sparrowlarks have a display song performed by males, a sub-song sung by both sexes and various different calls used in different contexts, e.g. flight and alarm calls. The study also presents the first analysis and description of the vocalizations of nestlings. An interesting feature of the vocalizations of the chestnut-backed sparrow-larks was that they performed hetero-specific vocal mimicry, which was incorporated in the subsong. Moult is a relatively unknown aspect in the annual cycle of the majority of larks. Chestnut-backed sparrow-larks undergo post-breeding moult, which is an adaptation to reduce the conflict between moult and breeding as both activities have high energy demands. The moult study also showed that they undergo a partial moult in mid-winter, involving the inner-most secondaries and some of the contour feathers. The results of this study shed valuable light on the natural history of this species and contributed significantly to ornithology and our growing understanding of the biology and ecology of the family. The results can also form a basis for future inter- and intraspecific comparative studies. The study illustrates the importance of undertaking long term studies of species to account for inter-annual differences in various ecological parameters.

Ammomanes cinctura (Bar-tailed Lark) is a lark species with a wide distribution in the Palearctic. One of its subspecies, A. c. arenicolor, has a wide range across northern Africa, within which it shows very minor morphological variation but deep divergence in the mitochondrial cytochrome b locus between two geographically widely separated populations. There are two additional allopatric subspecies, A. c. cinctura (Cape Verde Islands) and A. c. zarudnyi (Iran to Pakistan), which differ slightly more in morphology. The genomic population structure, evolutionary history, and taxonomic status of the different populations within this species remain unclear. I applied an integrative approach, using genomic single nucleotide polymorphisms (SNPs), mtDNA and morphological data, to investigate the evolutionary divergence within Ammomanes cinctura. I acquired whole-genome sequence data from twelve individuals from Morocco (n=2), Saudi Arabia (n=7), and Iran (n=3), and performed phylogenetic and population structure analyses. Mitochondrial genomes were assembled and cytochrome b was extracted for phylogeny. Biometric measurements and quantified plumage analysis were conducted on museum specimens of all three subspecies. According to the mitochondrial data, the samples from Saudi Arabia and Iran form a clade that is deeply diverged (5.94 Mya, 95%HPD 3.15–8.95 Mya) from a clade comprising the samples from Morocco and Cape Verde Islands. In contrast, the nuclear SNPs recovered a very shallow divergence (0.095 Mya, 95%HPD 0.04-0.16 Mya) and weak population structure between the samples from Morocco vs. Saudi Arabia–Iran. Morphological results indicated that zarudnyi is slightly differentiated from the other two subspecies, with a larger body size, and the three subspecies are slightly divergent in plumage. The close similarity between Moroccan and Saudi Arabian birds in morphology was also confirmed, in conflict with the molecular data – highlighting the problem with trinomials in this case. The results suggest that the deep divergence in mitochondrial DNA is due to a complex evolutionary history.

The Raso lark is a Critically Endangered bird endemic to the islet of Raso, Cape Verde. This thesis investigates two phenomena that particularly put the species at risk: its extreme fluctuations in population size, and its potentially very low genetic diversity arising from small population size and severe past population contraction. More specifically, two chapters estimate year-to-year survival and explore the factors - environmental and individual - that influence it, while two other chapters examine the lark’s genetic characteristics compared to its two continental closest relatives, including phylogenetic relationships and levels of genetic diversity. The conclusion of the thesis then uses these results to make recommendations for the conservation of the Raso lark. Each of the data chapters is summarized below: Chapter 3 estimates adult survival in the Raso lark and tests whether it could be linked to two population phenomena observed in the field: a highly variable population size and a male-biased sex ratio in certain years. Using a dataset spanning 10 years, I estimated survival for both sexes to fluctuate between 0.76 and 0.94 over this period. This is much higher than the survival rate of its closest relative, the skylark. I also found strong evidence for survival fluctuating over time and differing between males and females (with males having higher survival until 2011, at which point the trend inverted), which could play a role in the aforementioned population size fluctuations and male-biased sex ratio, respectively. Chapter 4 aims at understanding which factors shape survival in the Raso lark. Two types of variables were considered: year-dependent (rainfall, population size, population mean clutch size) and individual-dependent (age, body size characters, size ratio with mate, Ase18 genotype). Amongst the year-dependent variables, only sameyear rainfall impacted survival, with a 13% decrease in survival in the wettest year compared to the driest year, making it the most likely explanation for the inter-annual fluctuations in survival found in Chapter 3. Results also hint at some of the individual factors - morphological measurements and Ase18 genotype - influencing survival. The picture that emerges is that of a species whose life history strategy is to invest heavily in maintenance and survival, but less into fecundity, which stands in sharp contrast with the mainland-dwelling skylark. This is consistent with the theory that island birds generally have slower life history strategies than their continental counterparts. Chapter 5 determines the precise relationship between members of the Alauda clade, resolving a node on the phylogenetic tree of all larks that the study by Alström et al. (2013) was unable to resolve. My RADseq results indicate that the Raso lark and the skylark are sister species, and that the Oriental lark is likely to be a subpopulation, or maybe a subspecies, of the skylark. Chapter 6 compares the population genetics of the Raso lark with those of the skylark. In particular, it estimates the genetic diversity of the Raso lark and investigates the drivers behind it. I found unexpectedly high nucleotide diversity in the Raso lark, and explain this by showing that the population contraction that the species underwent was recent enough for most of the diversity to still be present. Moreover, 16% of the Raso lark genome has levels of heterozygosity on average 6.6 times higher than elsewhere on the genome, likely due to suppressed recombination and the existence of a neo-sex chromosome in larks. Despite this, I found high levels of relatedness and of linkage disequilibrium in the Raso lark, two clear genetic signs that it underwent a severe population contraction several centuries ago.