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Background In the speciation continuum, the strength of reproductive isolation varies, and species boundaries are blurred by gene flow. Interbreeding among giraffe ( Giraffa spp.) in captivity is known, and anecdotal reports of natural hybrids exist. In Kenya, Nubian ( G. camelopardalis camelopardalis ), reticulated ( G. reticulata ), and Masai giraffe sensu stricto ( G. tippelskirchi tippelskirchi ) are parapatric, and thus, the country might be a melting pot for these taxa. We analyzed 128 genomes of wild giraffe, 113 newly sequenced, representing these three taxa. Results We found varying levels of Nubian ancestry in 13 reticulated giraffe sampled across the Laikipia Plateau most likely reflecting historical gene flow between these two lineages. Although comparatively weaker signs of ancestral gene flow and potential mitochondrial introgression from reticulated into Masai giraffe were also detected, estimated admixture levels between these two lineages are minimal. Importantly, contemporary gene flow between East African giraffe lineages was not statistically significant. Effective population sizes have declined since the Late Pleistocene, more severely for Nubian and reticulated giraffe. Conclusions Despite historically hybridizing, these three giraffe lineages have maintained their overall genomic integrity suggesting effective reproductive isolation, consistent with the previous classification of giraffe into four species.

Giraffe (Giraffa spp.) numbers and their habitat have drastically declined throughout Africa over the last century due to various threats linked to anthropogenic impacts including habitat loss and fragmentation, disease, poaching, and climate change. In Kenya, the Nubian giraffe (G. camelopardalis camelopardalis) population decreased significantly up until the late 1980s. As a result of increased conservation efforts, the Nubian giraffe population has rebounded since the early 1990s, however, it remains predominantly extralimital and/or restricted to closed protected areas in central and western Kenya. In this paper, we set out to assess historical and current population numbers and trends of Nubian giraffe in Kenya, and highlight the conservation efforts that are applied to conserve this Critically Endangered taxon. We reviewed published manuscripts and grey literature, wildlife authority records and interviewed landowners with Nubian giraffe populations. We also conducted photographic surveys in three national parks and reserves where anecdotal reports suggested that the largest populations of Nubian giraffe occurred. We found that from a low of  130 individuals remaining in the wild and near extinction in the mid-1970s, the Nubian giraffe population has rebounded to  1,042 in 14 populations in Kenya, which represents an increase of more than 700%. This conservation success story is attributed to targeted management efforts, in particular conservation translocations and the increased monitoring of populations. At the same time, various factors including habitat loss and fragmentation, and infrastructure developments, linked with the increasing human population continue to pose a threat to their survival in the country. We place our findings in the broader context of population ecology and present opportunities for conservation research as well as recommendations that inform the management of this critical population of concern.

Historically, giraffe have been translocated across Africa to supplement extant populations, reintroduce extinct populations or to establish new populations, often for conservation and tourism. Such faunal relocations were often carried out disregarding taxonomic affiliation. Today, the small giraffe populations in the Republic of Malawi are assumed to consist of South African giraffe (Giraffa giraffa giraffa), which have likely descended from five individuals translocated from Imire Game Park (Zimbabwe) to Nyala Game Park (Malawi) in 1993. However, during the last 25 years, unknown additional translocations, migrations or unrecognized local populations of potential Masai giraffe (Giraffa tippelskirchi) in Malawi may have resulted in introgressive hybridization. Thus, the current taxonomic affiliation for Malawi’s giraffe is uncertain, calling for a genetic assessment to implement further management. We analyzed mitochondrial sequences and nuclear introns for 14 individuals, representing approximately half of the known Malawian population, to genetically determine the (sub)species of giraffe that occur in the Republic of Malawi by comparison with a comprehensive Giraffa dataset. Additionally, we genotyped individuals at ten microsatellite loci to determine the level of inbreeding and potential introgression. All data identify individuals unambiguously as South African giraffe, although two individuals shared a single nuclear allele with Masai giraffe. The low microsatellite genetic variability suggests high inbreeding in the current population. Thus, supplementing Malawi’s giraffe populations with G. g. giraffa will prevent further loss of their genetic diversity and avoid inbreeding depression.

The front feet of six adult free-ranging southern giraffe (Giraffa giraffa ) were opportunistically examined to characterize normal hoof anatomy, focusing on the corium (dermis), which provides vascular supply, metabolic support, and structural templates for the overlying epidermis that generates the keratinized hoof capsule. Gross dissection and histology identified two types of corium on the surface of the distal phalanx (Pd): laminae and papillae. On the parietal surface of Pd, laminae covered approximately its distal two-thirds and, as in other ruminants, secondary laminae were absent. Papillae varied regionally, with the longest and thickest located at the distal margins of Pd. On the solar surface, horn tubules were oriented obliquely in a palmar-proximal to dorso-distal direction. Within the hoof, the digital cushion consisted of a proximal adipose-rich region and a distal fibroelastic region. Histological findings were unremarkable and supported gross observations of normal anatomy. Examination of Pd and the navicular (distal sesamoid) regions revealed no evidence of pedal osteitis, navicular pathology, laminitis, or other lesions. These data provide a reference for normal giraffe foot anatomy and histology. Improved understanding of the corium and associated structures that support hoof capsule growth may inform preventative hoof care, reduce risk of overgrowth, and assist in managing lameness in both zoo-housed and free-ranging giraffe.

Behavioral plasticity, or the mechanism by which an organism can adjust its behavior in response to exogenous change, has been highlighted as a potential buffer against extinction risk. Giraffes (Giraffa spp.) are gregarious, long-lived, highly mobile megaherbivores with a large brain size, characteristics that have been associated with high levels of behavioral plasticity. However, while there has been a recent focus on genotypic variability and morphological differences among giraffe populations, there has been relatively little discussion centered on behavioral flexibility within giraffe populations. In large wild herbivores, one measure of behavioral plasticity is the ability to adjust herd size in line with local environmental conditions. Here, we examine whether a genetically isolated population of Angolan giraffes (G. g. angolensis) in a heterogeneous environment adjust their herd sizes in line with spatiotemporal variation in habitat. Our results suggest that ecological factors play a role in driving herd size, but that social factors also shape and stabilize herd-size dynamics. Specifically, we found that 1) mixed-sex herds were larger than single-sex herds, suggesting that sexual composition of herds played a role in driving herd size; 2) the presence of young did not influence herd size, suggesting that giraffes did not make use of the dilution effect to safeguard their young from predation; and 3) there was a strong relationship between herd size and spatial, but not seasonal, variation in food biomass availability, suggesting stability in herd sizes over time, but temporary variation in line with resource availability. These findings indicate that giraffes adjust herd size in line with local exogenous factors, signaling high behavioral plasticity, but also suggest that this mechanism operates within the constraints of the social determinants of giraffe herd size.

ContextReduced connectivity across grassland ecosystems can impair their functional heterogeneity and negatively impact large herbivore populations. Maintaining landscape connectivity across human-dominated rangelands is therefore a key conservation priority.ObjectiveIntegrate data on large herbivore occurrence and species richness with analyses of functional landscape connectivity to identify important areas for maintaining or restoring connectivity for large herbivores.MethodsThe study was conducted on a landscape with a mosaic of multiple land uses in Laikipia County, Kenya. We used occupancy estimates for four herbivore species [African elephant (Loxodonta africana), reticulated giraffe (Giraffa reticulata), plains zebra (Equus quagga), and Grevy’s zebra (Equus grevyi)] and species richness estimates derived from aerial surveys to create resistance surfaces to movement for single species and a multi-species assemblage, respectively. We validated single-species resistance surfaces using telemetry data. We used circuit theory and least cost-path analyses to model linkage zones across the landscape and prioritize areas for connectivity restoration.ResultsResistance layers approximated the movements of our focal species. Results for single-species and multi-species connectivity models were highly correlated (rp > 0.9), indicating similar spatial patterns of functional connectivity between individual species and the larger herbivore assemblage. We identified critical linkage zones that may improve permeability to large-herbivore movements.ConclusionOur analysis highlights the utility of aerial surveys in modeling landscape connectivity and informing conservation management when animal movement data are scarce. Our results can guide management decisions, providing valuable information to evaluate the trade-offs between improving landscape connectivity and safeguarding livelihoods with electrified fences across rangelands.

Masai (Giraffa tippelskirchi), Reticulated (G. reticulata) and Rothschild's (G. camelopardalis) giraffe lineages in East Africa are morphologically and genetically distinct, yet in Kenya their ranges abut. This raises the question of how divergence is maintained among populations of a large mammal capable of long-distance travel, and which readily hybridize in zoos. Here we test four hypotheses concerning the maintenance of the phylogeographic boundaries among the three taxa: 1) isolation-by-distance; 2) physical barriers to dispersal; 3) general habitat differences resulting in habitat segregation; or 4) regional differences in the seasonal timing of rainfall, and resultant timing of browse availability. We used satellite remotely sensed and climate data to characterize the environment at the locations of genotyped giraffes. Canonical variate analysis, random forest algorithms, and generalized dissimilarity modelling were employed in a landscape genetics framework to identify the predictor variables that best explained giraffes' genetic divergence. We found that regional differences in the timing of precipitation, and resulting green-up associated with the abundance of browse, effectively discriminate between taxa. Local habitat conditions, topographic and human-induced barriers, and geographic distance did not aid in discriminating among lineages. Our results suggest that selection associated with regional timing of events in the annual climatic cycle may help maintain genetic and phenotypic divergence in giraffes. We discuss potential mechanisms of maintaining divergence, and suggest that synchronization of reproduction with seasonal rainfall cycles that are geographically distinct may contribute to reproductive isolation. Coordination of weaning with green-up cycles could minimize the costs of lactation and predation on the young. Our findings are consistent with theory and empirical results demonstrating the efficacy of seasonal or phenologically dictated selection pressures in contributing to the reproductive isolation of parapatric populations.

Reproductive phenology (timing) is a heritable trait that confers a range of fitness or survival advantages. Giraffe (Giraffa spp.) breed year-round; however, some studies have suggested adaptive birth pulses, where demanding stages of reproduction coincide with seasonal increases in resource availability (phenological match). Here we use 3.5 years of demographic data to investigate the sociosexual behaviour and reproductive phenology of Angolan giraffe (G. g. angolensis) in the hyper arid northern Namib Desert, Namibia. We show that, in a highly seasonal desert ecosystem, giraffe gave birth to significantly more calves during the wet season. These calves were more likely to survive their first year of life, suggesting that season of birth may convey a fitness advantage. Furthermore, we show a decrease in sexual segregation between dominant (dark) adult males and adult females during the hot-dry season, suggesting a possible hot-dry season conception pulse. Finally, we demonstrate that the strongest correlation between the temporal pattern of births (wet-season pulse) and that of decreased sexual segregation (hot-dry season pulse) was time lagged by 15 months. This time lag corresponds to the period of gestation in giraffe, suggesting that a seasonal reduction in sexual segregation in this population may explain a seasonal birth pulse. These findings add to a sparse literature on the breeding phenology of giraffe, of asynchronously breeding megaherbivores, and of species with a gestation period of greater than 1 year. Results are discussed in terms of the possible environmental drivers of both season of conception and season of birth in this population. Furthermore, we highlight how predicted increases in seasonal instability due to climate change could reduce any putative fitness advantage associated with earlier birth dates.

All giraffe (Giraffa) were previously assigned to a single species (G. camelopardalis) and nine subspecies. However, multi‐locus analyses of all subspecies have shown that there are four genetically distinct clades and suggest four giraffe species. This conclusion might not be fully accepted due to limited data and lack of explicit gene flow analyses. Here, we present an extended study based on 21 independent nuclear loci from 137 individuals. Explicit gene flow analyses identify less than one migrant per generation, including between the closely related northern and reticulated giraffe. Thus, gene flow analyses and population genetics of the extended dataset confirm four genetically distinct giraffe clades and support four independent giraffe species. The new findings support a revision of the IUCN classification of giraffe taxonomy. Three of the four species are threatened with extinction, and mostly occurring in politically unstable regions, and as such, require the highest conservation support possible. Multi‐locus analyses of all giraffe (Giraffa camelopardalis) subspecies suggest four giraffe species. Our extended study based on 21 nuclear loci from 137 individuals, confirms four distinct species of giraffe based on explicit gene flow and population genetic analyses. The new findings call for a revision of the IUCN classification of giraffe taxonomy.

Three of the four species of giraffe are threatened, particularly the northern giraffe (Giraffa camelopardalis), which collectively have the smallest known wild population estimates. Among the three subspecies of the northern giraffe, the West African giraffe (Giraffa camelopardalis peralta) had declined to 49 individuals by 1996 and only recovered due to conservation efforts undertaken in the past 25 years, while the Kordofan giraffe (Giraffa camelopardalis antiquorum) remains at <2300 individuals distributed in small, isolated populations over a large geographical range in Central Africa. These combined factors could lead to genetically depauperated populations. We analyzed 119 mitochondrial sequences and 26 whole genomes of northern giraffe individuals to investigate their population structure and assess the recent demographic history and current genomic diversity of West African and Kordofan giraffe. Phylogenetic and population structure analyses separate the three subspecies of northern giraffe and suggest genetic differentiation between populations from eastern and western areas of the Kordofan giraffe’s range. Both West African and Kordofan giraffe show a gradual decline in effective population size over the last 10 ka and have moderate genome-wide heterozygosity compared to other giraffe species. Recent inbreeding levels are higher in the West African giraffe and in Kordofan giraffe from Garamba National Park, Democratic Republic of Congo. Although numbers for both West African and some populations of Kordofan giraffe have increased in recent years, the threat of habitat loss, climate change impacts, and illegal hunting persists. Thus, future conservation actions should consider close genetic monitoring of populations to detect and, where practical, counteract negative trends that might develop.