Reconciling apparent conflicts between mitochondrial and nuclear phylogenies in African elephants

Conservation strategies for African elephants would be advanced by resolution of conflicting claims that they comprise one, two, three or four taxonomic groups, and by development of genetic markers that establish more incisively the provenance of confiscated ivory. We addressed these related issues by genotyping 555 elephants from across Africa with microsatellite markers, developing a method to identify those loci most effective at geographic assignment of elephants (or their ivory), and conducting novel analyses of continent-wide datasets of mitochondrial DNA. Results showed that nuclear genetic diversity was partitioned into two clusters, corresponding to African forest elephants (99.5% Cluster-1) and African savanna elephants (99.4% Cluster-2). Hybrid individuals were rare. In a comparison of basal forest "F" and savanna "S" mtDNA clade distributions to nuclear DNA partitions, forest elephant nuclear genotypes occurred only in populations in which S clade mtDNA was absent, suggesting that nuclear partitioning corresponds to the presence or absence of S clade mtDNA. We reanalyzed African elephant mtDNA sequences from 81 locales spanning the continent and discovered that S clade mtDNA was completely absent among elephants at all 30 sampled tropical forest locales. The distribution of savanna nuclear DNA and S clade mtDNA corresponded closely to range boundaries traditionally ascribed to the savanna elephant species based on habitat and morphology. Further, a reanalysis of nuclear genetic assignment results suggested that West African elephants do not comprise a distinct third species. Finally, we show that some DNA markers will be more useful than others for determining the geographic origins of illegal ivory. These findings resolve the apparent incongruence between mtDNA and nuclear genetic patterns that has confounded the taxonomy of African elephants, affirm the limitations of using mtDNA patterns to infer elephant systematics or population structure, and strongly support the existence of two elephant species in Africa.     

Patterns of molecular genetic variation among African elephant populations

The highly threatened African elephants have recently been subdivided into two species, Loxodonta africana (savannah or bush elephant) and L. cyclotis (forest elephant) based on morphological and molecular studies. A molecular genetic assessment of 16 microsatellite loci across 20 populations (189 individuals) affirms species level genetic differentiation and provides robust genotypic assessment of species affiliation. Savannah elephant populations show modest levels of phylogeographic subdivision based on composite microsatellite genotype, an indication of recent population isolation and restricted gene flow between locales. The savannah elephants show significantly lower genetic diversity than forest elephants, probably reflecting a founder effect in the recent history of the savannah species.     

Relatedness and demography of African forest elephants: inferences from noninvasive fecal DNA analyses

African forest elephants (Loxodonta cyclotis) are genetically and morphologically distinct from their savannah counterparts, but their biology remains poorly understood. In this study, I use noninvasive fecal DNA analyses to examine the relatedness structure and historical demography of forest elephants at 2 sites in SW Gabon, central Africa. Pairwise relatedness values calculated between 162 elephant individuals genotyped at 8 microsatellite loci were significantly higher within spatially associated dung piles than between random pairings for one site. First- and second-order relatives were most commonly detected among dung piles from adult female pairs and adult females and juveniles. Pairwise relatedness estimates suggested that, like savannah elephants, forest groups are largely composed of adult females, their sisters, and juvenile offspring. Associations between males, and groups containing juveniles from multiple related females, were detected but at much lower frequency. Analysis of mitochondrial d-loop sequences from 70 elephant individuals identified 2 haplogroups in SW Gabon.     

Origin and phylogeography of African savannah elephants (<Emphasis Type="Italic">Loxodonta africana</Emphasis>) in Kruger and nearby parks in southern Africa

African savannah elephants (Loxodonta africana) occur in fragmented and isolated populations across southern Africa. Transfrontier conservation efforts aim at preventing the negative effects of population fragmentation by maintaining and restoring linkages between protected areas. We sought to identify genetic linkages by comparing the elephants in Kruger National Park (South Africa) to populations in nearby countries (Botswana, Mozambique, Zambia and Zimbabwe). We used a 446 base pair mitochondrial DNA (mtDNA) control region fragment (141 individuals) and 9 nuclear DNA (nDNA) microsatellite markers (69 individuals) to investigate phylogenetic relationships and gene flow among elephant populations. The mtDNA and nDNA phylogeographic patterns were incongruent, with mtDNA patterns likely reflecting the effects of ancient female migrations, with patterns persisting due to female philopatry, and nDNA patterns likely reflecting male-mediated dispersal. Kruger elephant heterozygosity and differentiation were examined, and were not consistent with genetic isolation, a depleted gene pool or a strong founder effect. Mitochondrial DNA geographic patterns suggested that the Kruger population was founded by elephants from areas both north and south of Kruger, or has been augmented through migration from more than one geographic source. We discuss our findings in light of the need for conservation initiatives that aim at maintaining or restoring connectivity among populations. Such initiatives may provide a sustainable, self-regulating management approach for elephants in southern Africa while maintaining genetic diversity within and gene flow between Kruger and nearby regions.     

Feeding patterns of elephants at the Atherstone Collaborative Nature Reserve

The African savannah elephant (Loxodonta africana Blumenbach) is a generalist herbivore that relies on widely distributed resources. Vegetation decline, aggravated by these elephants, can compromise local conservation efforts. Thus it imperative to understand the factors that drive them to consume specific plant species and plant parts. The objective of our study was to investigate the feeding patterns of African savannah elephants in the enclosed bushveld savannah at the Atherstone Collaborative Nature Reserve in South Africa. For 1 year, we examined elephant selection of woody versus herbaceous vegetation, and identified which plant species and parts were preferentially consumed. We accomplished this by directly observing feeding elephants, and by utilizing data collected on elephant footprints, dung piles, stripped bark and broken branches. We further conducted vegetation surveys to determine selection frequency relative to species abundance. Elephants showed a preference for different plant parts consumption in the feeding plots. In total, leaves, branches and bark contributed mostly to their diet. Seasonal selection patterns showed an increasing proportion of bark and branch consumption during the dry season.     

Contribution of molecular phylogeny and morphometrics to the systematics of African elephants

African elephants are conventionally classified as a single species: Loxodonta africana (Blumenbach 1797). However, the discovery in 1900 of a smaller form of the African elephant, spread throughout the equatorial belt of this land, has given rise to a debate over the relevance of a second species of elephant in Africa. The twentieth century has not provided any definite answer to this question. Actually, recent molecular analyses have sustained this issue by advocating either a division of forest elephants into a valid species, or their inclusion as a subspecies of L. africana. Our work initiated at the National Museum of Natural History of Paris provides new molecular (mitochondrial) and morphological (and morphometrical) evidence making it possible to propose a comprehensive phylogenetic hypothesis. It appears that there is no conclusive argument to keep forest elephants (cyclotis form) and savannah elephants (africana form) apart in two distinct species. A high level of mitochondrial introgression between the two forms, as well as a continuum in the morphology of the skulls of the two morphotypes rather suggests that, despite an ancient division, these two taxa freely interbreed wherever their ranges intersect. We thus adopt a conservative systematic position in considering these two forms as two subspecies, respectively: L. africana africana, the savannah elephant, and L. africana cyclotis, the forest elephant. We finally discuss the conservation topic in the light of this systematic framework.     

Status of the so-called African pygmy elephant (Loxodonta pumilio (NOACK 1906)): phylogeny of cytochrome b and mitochondrial control region sequences

Among the African elephants, it has been unanimously acknowledged that the forest elephants (cyclotis form) are peculiar, so that they have been elevated to the specific rank. The development of molecular analyses of extant Loxodonta has only focused on two forms yet: the savannah form (africana) and the forest form (cyclotis), disregarding the so-called pygmy elephants (pumilio or fransseni) the systematic status of which has been debated since their discovery. Therefore, we have sampled nine dwarfed-labelled specimens in collection and eight specimens of typical forest elephants that we compared to three savannah elephants and two Asian elephants. Because of the degraded nature of the nuclear DNA content in bone samples of old specimens, we assayed mitochondrial markers; 1961 bp of the mitochondrial genome were sequenced (over a continuous range spanning the cytochrome b gene, tRNA Thr, tRNA Pro, hypervariable region 1 and central conserved region of the control region). Pumilio and cyclotis are not sister-taxa: the phylogenetic analyses rather account for the inclusion of the so-called pygmy elephants within a monophyletic group of forest elephants sensu lato. The internal structure of this clade reveals to depend on isolation and remoteness between populations, characteristics that may have been extensively influenced by climatic variations during the Quaternary period. We conclude that the specific taxon Loxodonta pumilio (or Loxodonta fransseni) should be abandoned.     

A case study of apparent conflict between molecular phylogenies: the interrelationships of African elephants

Recent molecular phylogenies of the African elephants suggest that there is an evolutionary structure within Loxodonta africana. Some nuclear results ( Roca et al., 2001 ) support the separation of the forest African elephant subspecies L. a. cyclotis as a species distinct from the savannah elephant L. a. africana, on the basis of the recognition of both forming highly divergent (reciprocally monophyletic) clades. Conversely, a mitochondrial survey ( Eggert et al., 2002 ), while admitting a geographic partitioning of the genetic structure within African elephants, suggests retaining the status quo. They recognize three diagnosible entities (western, central and south‐eastern Africa) with non‐overlapping ranges within L. africana sensu lato. In order to address these conflicting views (historical fragmentation and speciation or isolation by distance, respectively), we have sequenced two datasets of 1961 bp (for 50 elephants) and about 3700 bp, respectively (for 20 elephants) of the mitochondrial DNA for both forms of elephants (cyclotis and africana). They span the cytochrome b gene, the control region and several RNAs. When compared with former mtDNA data, they provide the most comprehensive view of the African elephant phylogeny (78 mtDNA haplotypes, of which 44 are new) and provide the first insight into populations from the Democratic Republic of Congo. The genetic diversity of mtDNA was appraised and the stability of alternative phylogenetic trees was investigated. Our results are inconsistent with both those prior studies. They revealed two highly divergent molecular clades referred to as F and S, that do not conform to the morphological delineations of cyclotis and africana. A non‐negligible proportion of specimens of L. a. africana display haplotypes prevailing in forest elephant populations (clade F). The geographic distribution of clades and areas of their co‐occurrence support the hypothesis of incomplete isolation between forest and savannah African elephant populations, followed by recurrent interbreeding between the two forms. We state that the conclusions of prior studies resulted from insufficient character and/or geographic sampling. We conclude that there is no satisfying argument which can recognize two or more species of African elephants. We briefly comment on the meaning of such an attitude in a conservation viewpoint. © The Willi Hennig Society 2005.     

Characterization of tetranucleotide microsatellite loci in the African Savannah Elephant (Loxodonta africana africana)

Most African elephant (Loxodonta africana africana) populations are isolated and thus threatened by a loss of genetic diversity. As a consequence, genetic analysis of African elephant populations will play an increasing role in their conservation, and microsatellite loci will be an important tool in these analyses. Previously published sets of polymorphic microsatellites developed for African elephants are all dinucleotide repeats, which are prone to typing error. Here, we characterize 11 tetranucleotide microsatellite loci in the African elephant. All loci were polymorphic in 32 faecal samples and two tissue samples from 33 individual African savannah elephants.     

Forest elephant mitochondrial genomes reveal that elephantid diversification in Africa tracked climate transitions

Among elephants, the phylogeographic patterns of mitochondrial (mt) and nuclear markers are often incongruent. One hypothesis attributes this to sex differences in dispersal and in the variance of reproductive success. We tested this hypothesis by examining the coalescent dates of genetic markers within elephantid lineages, predicting that lower dispersal and lower variance in reproductive success among females would have increased mtDNA relative to nuclear coalescent dates. We sequenced the mitochondrial genomes of two forest elephants, aligning them to mitogenomes of African savanna and Asian elephants, and of woolly mammoths, including the most divergent mitogenomes within each lineage. Using fossil calibrations, the divergence between African elephant F and S clade mitochondrial genomes (originating in forest and savanna elephant lineages, respectively) was estimated as 5.5 Ma. We estimated that the (African) ancestor of the mammoth and Asian elephant lineages diverged 6.0 Ma, indicating that four elephantid lineages had differentiated in Africa by the Miocene–Pliocene transition, concurrent with drier climates. The coalescent date for forest elephant mtDNAs was c. 2.4 Ma, suggesting that the decrease in tropical forest cover during the Pleistocene isolated distinct African forest elephant lineages. For all elephantid lineages, the ratio of mtDNA to nuclear coalescent dates was much greater than 0.25. This is consistent with the expectation that sex differences in dispersal and in variance of reproductive success would have increased the effective population size of mtDNA relative to nuclear markers in elephantids, contributing to the persistence of incongruent mtDNA phylogeographic patterns.     

Genetic identification of five strongyle nematode parasites in wild african elephants (Loxodonta africana)

African savannah elephants (Loxodonta africana) are an ecologically and economically important species in many African habitats. However, despite the importance of elephants, research on their parasites is limited, especially in wild populations. Currently, we lack genetic tools to identify elephant parasites. We present genetic markers from ribosomal DNA (rDNA) and mitochondrial DNA (mtDNA) to identify five elephant-specific nematode parasites in the family Strongylidae: Murshidia linstowi, Murshidia longicaudata, Murshidia africana, Quilonia africana, and Khalilia sameera. We collected adult nematodes from feces deposited by wild elephants living in Amboseli National Park, Kenya. Using both morphologic and genetic techniques, we found that the internal transcribed spacer (ITS) region in rDNA provides a reliable marker to distinguish these species of strongyles. We found no evidence for cryptic genetic species within these morphologic species according to the cox-1 region of mtDNA. Levels of genetic diversity in strongyles from elephants were consistent with the genetic diversity seen within other strongyle species. We anticipate that these results will be a useful tool for identifying gastrointestinal nematode parasites in elephants.     

Evolutionary and demographic processes shaping geographic patterns of genetic diversity in a keystone species,the African forest elephant (Loxodonta cyclotis)

The past processes that have shaped geographic patterns of genetic diversity may be difficult to infer from current patterns. However, in species with sex differences in dispersal, differing phylogeographic patterns between mitochondrial (mt) and nuclear (nu) DNA may provide contrasting insights into past events. Forest elephants (Loxodonta cyclotis) were impacted by climate and habitat change during the Pleistocene, which likely shaped phylogeographic patterns in mitochondrial (mt) DNA that have persisted due to limited female dispersal. By contrast, the nuclear (nu) DNA phylogeography of forest elephants in Central Africa has not been determined. We therefore examined the population structure of Central African forest elephants by genotyping 94 individuals from six localities at 21 microsatellite loci. Between forest elephants in western and eastern Congolian forests, there was only modest genetic differentiation, a pattern highly discordant with that of mtDNA. Nuclear genetic patterns are consistent with isolation by distance. Alternatively, male‐mediated gene flow may have reduced the previous regional differentiation in Central Africa suggested by mtDNA patterns, which likely reflect forest fragmentation during the Pleistocene. In species like elephants, male‐mediated gene flow erases the nuclear genetic signatures of past climate and habitat changes, but these continue to persist as patterns in mtDNA because females do not disperse. Conservation implications of these results are discussed.     

Identifying Source Populations and Genetic Structure for Savannah Elephants in Human-Dominated Landscapes and Protected Areas in the Kenya-Tanzania Borderlands

We investigated the genetic metapopulation structure of elephants across the trans Rift Valley region of Kenya and Tanzania, one of the remaining strongholds for savannah elephants (Loxodonata africana) in East Africa, using microsatellite and mitochondrial DNA (mtDNA) markers. We then examined this population structure to determine the source population for a recent colonization event of savannah elephants on community-owned land within the trans rift valley region. Four of the five sampled populations showed significant genetic differentiation (p<0.05) as measured with both mtDNA haplotypes and microsatellites. Only the samples from the adjacent Maasai Mara and Serengeti ecosystems showed no significant differentiation. A phylogenetic neighbour-joining tree constructed from mtDNA haplotypes detected four clades. Clade four corresponds to the F clade of previous mtDNA studies that reported to have originated in forest elephants (Loxodonta cyclotis) but to also be present in some savannah elephant populations. The split between clade four and the other three clades corresponded strongly to the geographic distribution of mtDNA haplotypes across the rift valley in the study area. Clade four was the dominant clade detected on the west side of the rift valley with rare occurrences on the east side. Finally, the strong patterns of population differentiation clearly indicated that the recent colonists to the community-owned land in Kenya came from the west side of the rift valley. Our results indicate strong female philopatry within the isolated populations of the trans rift valley region, with gene flow primarily mediated via male movements. The recent colonization event from Maasai Mara or Serengeti suggests there is hope for maintaining connectivity and population viability outside formal protected areas in the region.     

Major histocompatibility complex variation and evolution at a single, expressed DQA locus in two genera of elephants

Genes of the vertebrate major histocompatibility complex (MHC) are crucial to defense against infectious disease, provide an important measure of functional genetic diversity, and have been implicated in mate choice and kin recognition. As a result, MHC loci have been characterized for a number of vertebrate species, especially mammals; however, elephants are a notable exception. Our study is the first to characterize patterns of genetic diversity and natural selection in the elephant MHC. We did so using DNA sequences from a single, expressed DQA locus in elephants. We characterized six alleles in 30 African elephants (Loxodonta africana) and four alleles in three Asian elephants (Elephas maximus). In addition, for two of the African alleles and three of the Asian alleles, we characterized complete coding sequences (exons 1–5) and nearly complete non-coding sequences (introns 2–4) for the class II DQA loci. Compared to DQA in other wild mammals, we found moderate polymorphism and allelic diversity and similar patterns of selection; patterns of non-synonymous and synonymous substitutions were consistent with balancing selection acting on the peptides involved in antigen binding in the second exon. In addition, balancing selection has led to strong trans-species allelism that has maintained multiple allelic lineages across both genera of extant elephants for at least 6 million years. We discuss our results in the context of MHC diversity in other mammals and patterns of evolution in elephants.     

New evidence for hybrid zones of forest and savanna elephants in Central and West Africa

The African elephant consists of forest and savanna subspecies. Both subspecies are highly endangered due to severe poaching and habitat loss, and knowledge of their population structure is vital to their conservation. Previous studies have demonstrated marked genetic and morphological differences between forest and savanna elephants, and despite extensive sampling, genetic evidence of hybridization between them has been restricted largely to a few hybrids in the Garamba region of northeastern Democratic Republic of Congo (DRC). Here, we present new genetic data on hybridization from previously unsampled areas of Africa. Novel statistical methods applied to these data identify 46 hybrid samples – many more than have been previously identified – only two of which are from the Garamba region. The remaining 44 are from three other geographically distinct locations: a major hybrid zone along the border of the DRC and Uganda, a second potential hybrid zone in Central African Republic and a smaller fraction of hybrids in the Pendjari–Arli complex of West Africa. Most of the hybrids show evidence of interbreeding over more than one generation, demonstrating that hybrids are fertile. Mitochondrial and Y chromosome data demonstrate that the hybridization is bidirectional, involving males and females from both subspecies. We hypothesize that the hybrid zones may have been facilitated by poaching and habitat modification. The localized geography and rarity of hybrid zones, their possible facilitation from human pressures, and the high divergence and genetic distinctness of forest and savanna elephants throughout their ranges, are consistent with calls for separate species classification.     

Physiological indicators of stress in African forest elephants (Loxodonta africana cyclotis) in relation to petroleum operations in Gabon,Central Africa

Aim Human activities are major determinants of forest elephant (Loxodonta africana cyclotis) distribution in Gabon, but the types and intensity of disturbance that elephants can tolerate are not known. We conducted dung surveys within the Gamba Complex of Protected Areas in SW Gabon to examine (1) the feasibility of noninvasive faecal analyses for monitoring stress physiology, and (2) the influence of petroleum operations on stress levels in forest elephants. Location Gabon, Central Africa. Methods We identified multiple dung piles from the same individual by matching their eight‐locus microsatellite genotypes, and measured faecal concentrations of glucocorticoid metabolites as an indicator of stress in areas subject to different levels of disturbance: (1) Loango National Park (2) an ‘industrial corridor’ dominated by oil fields, and (3) a nearby area of human settlements. Results We obtained unique microsatellite genotypes and faecal glucocorticoid metabolite (FGM) concentrations for 150 forest elephant individuals, which is the largest hormonal data set for wild African forest elephants to date. Adults exhibited higher mean FGM concentrations than juveniles, and in contradiction of our expectations of chronic stress around oil fields, elephants in Loango National Park exhibited significantly higher FGM concentrations than elephants in the industrial corridor. Main conclusions We argue that forest elephants in the industrial corridor of the Gamba Complex have become acclimated to oil fields, resulting in part from oil company regulations that minimize stressful interactions between elephants and petroleum operations. Our findings for a flagship species with substantial ecological requirements bode well for other taxa, but additional studies are needed to determine whether oil operations are compatible over their life span with rain forest ecosystems in Central Africa.     

Small-scale dung survey reveals high forest elephant density and preference for mixed species forest in an intact protected area

Understanding the ecological factors influencing African forest elephant (Loxodonta cyclotis) abundance and distribution is crucial for their conservation management in Central Africa. Dung surveys have been conducted at the landscape scale and confirmed the overwhelming impact of anthropogenic activities on forest elephants. We present results from a small-scale survey in a pristine protected area without anthropogenic activities to elucidate the ecological factors influencing forest elephant density. We conducted a line transect dung survey in a small study area (110 km²) around Mbeli Bai, a natural forest clearing in the Nouabalé-Ndoki National Park, Republic of Congo, and compare results with a landscape survey conducted during the same period. We used habitat specific dung decay data collected on site to estimate elephant density using distance sampling. We fitted Generalized Additive Models to elephant dung encounter rate using explanatory variables collected during the transect survey and from geospatial data. The small-scale survey revealed a precise estimate of forest elephant density that was twice as high as the result from a landscape survey with higher density in mixed species forest for the small-scale survey. We could not find an impact of the proximity of forest clearings and proximity to rivers at the small scale. Fine-scale habitat features, e.g. degree of canopy and understorey closure, had little explanatory power for elephant dung encounter rate. Small-scale dung surveys are a useful method to reveal spatio-temporal variation in forest elephant density and distribution which can inform conservation practitioners in a timely manner. Combining monitoring methods at various spatial scales improves our knowledge and conservation efforts of forest elephants. Nouabalé-Ndoki National Park is a stronghold for forest elephants and of global importance for their conservation.

     

Skeletal development in the African elephant and ossification timing in placental mammals

We provide here unique data on elephant skeletal ontogeny. We focus on the sequence of cranial and post-cranial ossification events during growth in the African elephant (Loxodonta africana). Previous analyses on ossification sequences in mammals have focused on monotremes, marsupials, boreoeutherian and xenarthran placentals. Here, we add data on ossification sequences in an afrotherian. We use two different methods to quantify sequence heterochrony: the sequence method and event-paring/Parsimov. Compared with other placentals, elephants show late ossifications of the basicranium, manual and pedal phalanges, and early ossifications of the ischium and metacarpals. Moreover, ossification in elephants starts very early and progresses rapidly. Specifically, the elephant exhibits the same percentage of bones showing an ossification centre at the end of the first third of its gestation period as the mouse and hamster have close to birth. Elephants show a number of features of their ossification patterns that differ from those of other placental mammals. The pattern of the initiation of the ossification evident in the African elephant underscores a possible correlation between the timing of ossification onset and gestation time throughout mammals.     

Autosomal and mtDNA Markers Affirm the Distinctiveness of Lions in West and Central Africa

The evolutionary history of a species is key for understanding the taxonomy and for the design of effective management strategies for species conservation. The knowledge about the phylogenetic position of the lion (Panthera leo) in West/Central Africa is largely based on mitochondrial markers. Previous studies using mtDNA only have shown this region to hold a distinct evolutionary lineage. In addition, anthropogenic factors have led to a strong decline in West/Central African lion numbers, thus, the conservation value of these populations is particularly high. Here, we investigate whether autosomal markers are concordant with previously described phylogeographic patterns, and confirm the unique position of the West/Central African lion. Analysis of 20 microsatellites and 1,454 bp of the mitochondrial DNA in 16 lion populations representing the entire geographic range of the species found congruence in both types of markers, identifying four clusters: 1) West/Central Africa, 2) East Africa, 3) Southern Africa and 4) India. This is not in line with the current taxonomy, as defined by the IUCN, which only recognizes an African and an Asiatic subspecies. There are no indications that genetic diversity in West/Central Africa lions is lower than in either East or Southern Africa, however, given this genetic distinction and the recent declines of lion numbers in this region, we strongly recommend prioritization of conservation projects in West/Central Africa. As the current taxonomic nomenclature does not reflect the evolutionary history of the lion, we suggest that a taxonomic revision of the lion is warranted.     

A simple and accurate method to sex savannah, forest and Asian elephants using noninvasive sampling techniques

We report the development of a reliable and efficient method for molecular sexing of all extant elephant taxa. We developed primers that amplify two short Y-specific fragments (SRY1 and AMELY2) and one longer X-specific fragment (PLP1), developed from elephant sequences in one multiplex PCR. All fragments were designed to be short (< 200 basepairs) for use with degraded DNA and to be 50 basepairs apart to optimize visualization on agarose gels or as electropherograms. The multiplex PCR method matched sexes for at least 97.9% of the noninvasive savannah elephant samples and produced the expected female/male banding patterns for 14 African forest and 11 Asian elephant samples. We found this method to be more robust, efficient and less prone to contamination than previously developed sexing methods for elephants.