Evolutionary systematics in African gerbilline rodents of the genus Gerbilliscus: inference from mitochondrial genes

Gerbilliscus has recently been proposed as an endemic African rodent genus distinct from the Asian Tatera. A molecular phylogeny of the genus, including nine species from southern, western and eastern Africa, is presented here based on the analysis of the cytochrome b and 16S mitochondrial genes. With an adequate taxonomic sampling over a wide geographic range, we here provide a clear picture of the phylogenetic relationships between species and species groups in this genus. Three distinct clades were resolved, corresponding to major geographical subdivisions: an eastern clade that possibly diverged first, then a southern and a western clades which appeared later. We suggest two possible hypotheses concerning the dispersal of the genus across Africa, considering also the patterns of karyotypic variation. Finally, we discuss the taxonomic status of G. gambianus and the relationships between Gerbillurus and Gerbilliscus, as previous studies have suggested that the former should be included in the latter. Our data seem to support the synonymy of the two taxa and suggest that Gerbillurus and Gerbilliscus lineages diverged from a common ancestor appeared in eastern Africa.     

Mitochondrial Diversity and Distribution of African Green Monkeys (Chlorocebus Gray, 1870)

African green monkeys (Chlorocebus) represent a widely distributed and morphologically diverse primate genus in sub‐Saharan Africa. Little attention has been paid to their genetic diversity and phylogeny. Based on morphological data, six species are currently recognized, but their taxonomy remains disputed. Here, we aim to characterize the mitochondrial (mt) DNA diversity, biogeography and phylogeny of African green monkeys. We analyzed the complete mitochondrial cytochrome b gene of 126 samples using feces from wild individuals and material from zoo and museum specimens with clear geographical provenance, including several type specimens. We found evidence for nine major mtDNA clades that reflect geographic distributions rather than taxa, implying that the mtDNA diversity of African green monkeys does not conform to existing taxonomic classifications. Phylogenetic relationships among clades could not be resolved suggesting a rapid early divergence of lineages. Several discordances between mtDNA and phenotype indicate that hybridization may have occurred in contact zones among species, including the threatened Bale monkey (Chlorocebus djamdjamensis). Our results provide both valuable data on African green monkeys’ genetic diversity and evolution and a basis for further molecular studies on this genus. Am. J. Primatol. 75:350‐360, 2013. © 2013 Wiley Periodicals, Inc.     

Systematics and phylogeography of Acanthodactylus schreiberi and its relationships with Acanthodactylus boskianus (Reptilia: Squamata: Lacertidae)

Acanthodactylus is a widespread lacertid genus occurring from the Iberian Peninsula and western North Africa to western India including the Middle East, Cyprus, and the Arabian Peninsula. The genus is in dire need of a taxonomic revision, and the phylogenetic relationships amongst and within its species remain unclear. In particular, the taxonomy and relationship of the allopatric, narrow‐ranged Acanthodactylus schreiberi and its close relative, the widespread Acanthodactylus boskianus asper, are poorly understood. We estimated the phylogenetic and phylogeographical structure of A. schreiberi across its distribution range, and evaluated its relationships to A. b. asper, using mitochondrial and nuclear data. The phylogenetic results indicate that both species are paraphyletic, with A. schreiberi nested within A. b. asper, and the subspecies A. schreiberi syriacus nested within a distinct lineage of A. b. asper. We suggest that the group is in need of a taxonomic revision because the identified lineages and genetic diversity are incongruent with the currently recognized taxonomy. We tentatively conclude that A. schreiberi is restricted to Cyprus and Turkey, reduced to a single form, and that the populations in Lebanon and Israel belong to A. b. asper. © 2014 The Linnean Society of London     

Species-level diversification of African dwarf crocodiles (Genus Osteolaemus): A geographic and phylogenetic perspective

The taxonomy of the African dwarf crocodile (genus Osteolaemus) has been disputed since a novel morphotype was discovered in the early 20th Century. Because this poorly-known reptile is widely hunted throughout the forests of Central and West Africa, resolving the existence and extent of taxonomic units has important management and conservation implications. Lack of molecular data from individuals of known origin and historical disagreement on diagnostic morphological characters have hindered attempts to settle one of the most important taxonomic questions in the Crocodylia. In an effort to clarify the evolutionary relationships among dwarf crocodiles, we sequenced three mitochondrial and two nuclear genes using a large sample of dwarf crocodiles from known localities across major drainage basins of forested Africa. Concordant results from Bayesian, maximum likelihood, maximum parsimony and population aggregation analytical methods support a previously recognized division of the dwarf crocodile into a Congo Basin form (O. osborni) and a West African form (Osteolaemus tetraspis), but also reveal a third diagnosable lineage from West Africa warranting recognition as an separate taxonomic unit. Corrected genetic distances between geographic regions ranged from 0.2% to 0.6% in nuclear fragments and 10.0 to 16.2% in mitochondrial COI. Population aggregation, using fixed and alternate character (nucleotide) states to cluster or divide populations, recovered 232 such molecular characters in 4286 bp of sequence data and unambiguously aggregated populations into their respective geographic clade. Several previously recognized morphological differences coincide with our molecular analysis to distinguish Congo Basin crocodiles from the Ogooué Basin and West Africa. Discrete morphological characters have not yet been documented between the latter two regions, suggesting further work is needed or molecular data may be required to recognize taxonomic divisions in cases where putative species are morphologically cryptic. This study highlights the importance of using widespread taxon sampling and a multiple evidence approach to diagnose species boundaries and reveal cryptic diversity.     

Phylogeny and species reassessment of Hyalopterus (Aphididae,Aphidinae)

The broadly distributed genus Hyalopterus currently comprises three formally recognized species that are highly similar morphologically and hence difficult to be identified with certainty. This group has undergone multiple revisions in the past century, but none of these has assessed species from Asia, which has hampered our understanding of the species diversity within this genus. Based on a comprehensive data set from morphological data and host-associated data, and by coalescent-based delimitation approaches, the Hyalopterus species boundaries, distribution and diversity were clarified here to further reveal the composition of the species. Two single-locus (ML-GMYC and mPTP) and two multilocus (BPP and STACEY) delimitation methods were conducted based on extensive sampling. Then, the phylogenetic relationships and morphological divergence were assessed. Our data strongly supported that the number of recognized species in Hyalopterus had likely been underestimated. The phylogenetic analyses recovered four major clades, which corresponded to distinct host-plant preferences. Also, the morphological analyses showed significant differentiation for only one of the newly recognized candidate species uncovered by the delimitation approaches, suggesting the existence of at least two independent evolutionary lineages within Hyalopterus arundiniformis, which showed different patterns of host association. Moreover, based on our data, the taxonomic misidentification of H. arundiniformis in China was corrected here. This study lays the groundwork for the thorough taxonomic revision of Hyalopterus and for future evolutionary studies and underlines the importance of an integrated framework for species determination.     

Spatial analysis of taxonomic and genetic patterns and their potential for understanding evolutionary histories

Aim The aim of this research is to develop and investigate methods for the spatial analysis of diversity based on genetic and taxonomic units of difference. We use monophyletic groups of species to assess the potential for these diversity indices to elucidate the geographical components of macro‐scaled evolutionary processes. Location The range occupied by Pultenaea species in temperate and sub‐tropical eastern Australia, extending from western South Australia (133° E–32° S) to Tasmania (146° E–43° S) to coastal central Queensland (148° E–20° S). Methods We applied a series of both spatially explicit and spatially implicit analyses to explore the nature of diversity patterns in the genus Pultenaea, Fabaceae. We first analysed the eastern species as a whole and then the phylogenetic groups within them. We delineated patterns of endemism and biotic (taxon) regions that have been traditionally circumscribed in biogeographical studies of taxa. Centres of endemism were calculated using corrected weighted endemism at a range of spatial scales. Biotic regions were defined by comparing the similarity of species assemblages of grid cells using the Jaccard index and clustering similar cells using hierarchical clustering. On the basis that genetically coherent areas were likely to be more evolutionary informative than species patterns, genetic indices of similarity and difference were derived. A matrix of similarity distances between taxa was generated based on the number of shared informative characters of two sections of trnL‐F and ndhF chloroplast nuclear regions. To identify genetically similar areas, we clustered cells using the mean genetic similarities of the species contained within each pair of cells. Measures of the mean genetic similarity of species in areas were delineated using a geographically local multi‐scalar approach. Resultant patterns of genetic diversity are interpreted in relation to theories of the evolutionary relationships between species and species groups. Results Centres of Pultenaea endemism were defined, those of clades 1 congruent with the spatially separated centres of clades 2 and 3. The taxonomic classification analysis defined cells with shared groups of species, which in some cases clustered when plotted in geographic space, defining biotic regions. In some instances the distribution of biotic regions was congruent with centres of endemism, however larger scale groupings were also apparent. In clade 1 one set of species was replaced by another along the extent of the range, with some connectivity between some geographically disjunct regions due to the presence of widespread species. In the combined analysis of clade 2 and 3 species the major biotic (taxonomic) groups with geographic coherence were defined by species in the respective clades, representing the geographic separation of these clades. However distinctive biotic regions within these main groupings of clades 2 and 3 were also apparent. Clustering cells using the mean genetic similarities of the species contained within each pair of cells indicated that some of the taxonomically defined biotic boundaries were the result of changes in composition of closely related species. This was most apparent in clades 1 and 2 where most cells were highly genetically similar. In clade 3 genetically distinct groups remained and were in part defined by sister taxa with disjunct distributions. Gradients in mean genetic similarity became more apparent from small to larger scales of analysis. At larger scales of analysis, regions of different levels of genetic diversity were delineated. Regions with highest diversity levels (lowest level of similarity) often represented regions where the ranges of phylogenetically distinctive species intergraded. Main conclusions The combined analysis of diversity, phylogeny and geography has potential to reveal macro‐scaled evolutionary patterns from which evolutionary processes may be inferred. The spatial genetic diversity indices developed in this study contribute new methods for identifying coherent evolutionary units in the landscape, which overcome some of the limitations of using taxonomic data, and from which the role of geography in evolutionary processes can be tested. We also conclude that a multiple‐index approach to diversity pattern analysis is useful, especially where patterns may be the result of a long history of different environmental changes and related evolutionary events. The analysis contributes to the knowledge of large‐scale diversity patterns of Pultenaea which has relevance for the assessment of the conservation status of the genus.     

Molecular relationships in Encephalartos (Zamiaceae, Cycadales) based on nucleotide sequences of nuclear ITS 1&2, rbcL, and genomic ISSR fingerprinting

The cycad genus Encephalartos is restricted to Africa and is threatened with extinction in most of its range. Total DNA was extracted from 51, i.e., 78 %, of the described species of Encephalartos. The accessions were sampled from the furthest western occurrence of the genus in Nigeria, via Sudan and Uganda, to southern South Africa. The sequences of nuclear ribosomal internal transcribed spacer regions 1 and 2 (ITS 1&2), the chloroplast encoded rbcL gene, and ISSR genomic fingerprinting were employed to resolve the molecular history and the relationships within the genus. Sequence alignment, as well as ISSR fingerprinting, data show low genetic variation among all analysed accessions, indicating diversification within the Pliocene/Pleistocene. ITS 1&2 data agree well with morphological and geographical characters and resolved three major genetic clusters with overlapping distribution ranges in eastern South Africa. This area, that contains the largest diversity of genotypes of Encephalartos, may have served as a Pliocene/Pleistocene refugium.     

Phylogeny of Philippine slender skinks (Scincidae: Brachymeles) reveals underestimated species diversity, complex biogeographical relationships, and cryptic patterns of lineage diversification

The spectacular, virtually endemic radiation of Philippine semi-fossorial skinks of the genus Brachymeles represent one of the few radiations of scincid lizards to possess both fully limbed and limbless species. And yet, nothing is known of the phylogenetic relationships of this exceptional group. Morphologically similar body plans have made it difficult to assess species-level diversity, and the genus has long been recognized as one of the more modest radiations of southeast Asian lizards. However, recent large-scale survey efforts have resulted in the discovery of numerous new species, and taxonomic studies indicate that the diversity within the genus Brachymeles is grossly underestimated. In this study we provide the first robust estimate of phylogenetic relationships within the genus Brachymeles using a multi-locus dataset and nearly complete taxonomic sampling. We provide statistical tests of monophyly for all polytypic species and two widespread limb-reduced species and our results indicate wholesale deviations from past summaries and taxonomic evaluations of the genus. With few exceptions, we are able to reject the monophyly of all polytypic and widespread species, thereby validating the need for large-scale taxonomic revisions. Our results reveal that the limbless, monotypic, genus Davewakeum is nested within Brachymeles. Mapping of body form on our preferred phylogenetic tree suggests that limb-reduction and digit loss has occurred on multiple occasions in the history of the genus. A Bayesian reconstruction of ancestral areas indicates strong statistical support for a minimum of five major dispersal events that have given rise to a major component of the observed species diversity on separate Pleistocene aggregate island platforms of the archipelago.     

Chromosomal evidence for a polytypic structure of Arvicanthis niloticus (Rodentia, Muridae)

The analysis of R- and C-banding patterns of chromosomes of Arvicanthis niloticus from five localities of Africa (Egypt, Senegal, Burkina-Faso, Mali and Central African Republic) revealed the existence of three karyotypic forms labelled in the study as ANI-1, ANI-2 and ANI-3. These forms differ from each other by 6 to 8 chromosomal rearrangements such as reciprocal and Robertsonian translocations and pericentric inversions. Moreover, they possess different quantities of C-heterochromatin. The data indicate that these three forms are distinct species, cytogenetically isolated, and that a further taxonomic analysis of the genus Arvicanthis is needed.     

Evolutionary history of spiny‐tailed lizards (Agamidae: Uromastyx) from the Saharo‐Arabian region

The subfamily Uromastycinae within the Agamidae is comprised of 18 species: three within the genus Saara and 15 within Uromastyx. Uromastyx is distributed in the desert areas of North Africa and across the Arabian Peninsula towards Iran. The systematics of this genus has been previously revised, although incomplete taxonomic sampling or weakly supported topologies resulted in inconclusive relationships. Biogeographic assessments of Uromastycinae mostly agree on the direction of dispersal from Asia to Africa, although the timeframe of the cladogenesis events has never been fully explored. In this study, we analysed 129 Uromastyx specimens from across the entire distribution range of the genus. We included all but one of the recognized taxa of the genus and sequenced them for three mitochondrial and three nuclear markers. This enabled us to obtain a comprehensive multilocus time‐calibrated phylogeny of the genus, using the concatenated data and species trees. We also applied coalescent‐based species delimitation methods, phylogenetic network analyses and model‐testing approaches to biogeographic inferences. Our results revealed Uromastyx as a monophyletic genus comprised of five groups and 14 independently evolving lineages, corresponding to the 14 currently recognized species sampled. The onset of Uromastyx diversification is estimated to have occurred in south‐west Asia during the Middle Miocene with a later radiation in North Africa. During its Saharo‐Arabian colonization, Uromastyx underwent multiple vicariance and dispersal events, hypothesized to be derived from tectonic movements and habitat fragmentation due to the active continental separation of Arabia from Africa and the expansion and contraction of arid areas in the region.     

Towards understanding the dynamics of hybridization and apomixis in the evolution of the genus Boechera (Brassicaceae)

We have reviewed past and recent research on the radiation of the North American genus Boechera (Brassicaceae), and discuss future prospects for our understanding of the evolutionary processes and patterns of differentiation in this highly polymorphic genus. Boechera comprises about 80 biennial to perennial species of exclusively North American and Greenlandic distribution. Hybridization and apomixis, in conjunction with polyploidy, were found to play a major role in the origin and maintenance of intraspecific and interspecific polymorphism. However, taxonomic classification within the genus has mainly been based on morphological characters, and diagnostic features discriminating between taxa are often limited. Molecular markers are promising tools for: the assessment of infrageneric phylogen‐etic relationships, the isolation of basal sexual taxa, the detection of hybridization and estimation of its frequency among lineages in time and space, the identification of centres of genetic and species diversity, and the comparison of various reproductive modes. We present and discuss the major achievements obtained since the introduction of molecular methods to Boechera research with respect to these aims, and point out possible shortcomings of specific marker systems. The distribution and transmission of apomixis, polyphyletic origin of genotypes and cytotypes, variation in reproductive system, and the lack of consensus between current taxonomic concepts and evolutionary evidence are the major topics discussed here in the context of hybridization.     

Molecular diversity and distribution of eastern Atlantic and Mediterranean dogfishes Squalus highlight taxonomic issues in the genus

The alpha taxonomy of the globally distributed shark genus Squalus has been under intense investigation recently, and many new species have been described over the last decade. However, taxonomic uncertainty remains about several taxa. Without consistent nomenclature and the ability to reliably distinguish between the different Squalus species, basic data collection, downstream conservation and management efforts are seriously compromised. To aid in clarifying the taxonomic status of Squalus species in the eastern Atlantic and Mediterranean, we assessed species diversity at the molecular level and evaluated the consistency in species identification in the region. Samples from all nominal Squalus species recognized in the above regions were collected in an international effort and sequenced for regions of the mitochondrial COI and ND2 genes. These data were further analysed alongside publicly available sequences, including 19 of the 26 Squalus species globally recognized, to compare the regional genus‐level diversity with that found elsewhere. Our results confirm inconsistent species identification in the eastern Atlantic and Mediterranean Squalus, particularly concerning S. blainville and S. megalops, and reinforce the need to revise the status of S. megalops and S. mitsukurii as they may include several distinct species distributed around the world. The status of S. blainville is also discussed in the light of the current findings and its problematic taxonomic history.     

Taxonomic studies on marine triclads (Turbellaria,Tricladida, Maricola)

The genus Procerodes forms a heterogeneous assemblage of taxa. Although it is premature to attempt phylogenetic weighting of the characters, the genus contains three well delimited subgroups, one with a subantarctic, panaustral distribution, one world-wide in distribution, and one occurring principally in the northern hemisphere. Outside of these subgroups, species in this genus are problematic since a number of their features also occurs in other procerodids. All recognized groups exhibit a wide distributional range. Many of the world-wide taxonomic relations lie on the species level and some at the level of genera. Poor dispersal capacity of extant species of Procerodes suggests that the biogeographic patterns may be very old.     

Deep phylogeographic structure may indicate cryptic species within the Sparid genus Spondyliosoma

Two geographically nonoverlapping species are currently described within the sparid genus Spondyliosoma: Spondyliosoma cantharus (Black Seabream) occurring across Mediterranean and eastern Atlantic waters from NW Europe to Angola and S. emarginatum (Steentjie) considered endemic to southern Africa. To address prominent knowledge gaps this study investigated range-wide phylogeographic structure across both species. Mitochondrial DNA sequences revealed deep phylogeographic structuring with four regionally partitioned reciprocally monophyletic clades, a Mediterranean clade and three more closely related Atlantic clades [NE Atlantic, Angola and South Africa (corresponding to S. emarginatum)]. Divergence and distribution of the lineages reflects survival in, and expansion from, disjunct glacial refuge areas. Cytonuclear differentiation of S. emarginatum supports its validity as a distinct species endemic to South African waters. However, the results also indicate that S. cantharus may be a cryptic species complex wherein the various regional lineages represent established/incipient species. A robust multilocus genetic assessment combining morphological data and detailing interactions among lineages is needed to determine the full diversity within Spondyliosoma and the most adequate biological and taxonomic status.     

Chromosomal diversity in the genus Arvicanthis (Rodentia, Muridae) from East Africa: a taxonomic and phylogenetic evaluation

In this paper we discuss the contribution of cytogenetics to the systematics of Arvicanthis in East Africa, by reviewing all the known chromosomal cytotypes of the genus in the area. We also provide G‐ and C‐banding comparisons for two recently described karyotypes, provisionally named ANI‐5 (2n = 56, NFa = 62) and ANI‐6 (2n = 60, NFa = 72). This, therefore, brings the total number of known cytotypes in this area to 10. Five of these correspond to the species recognized by the latest rodent checklist, i.e. A. nairobae (2n = 62, NFa = 78), A. neumanni (2n = 52–53, NFa = 62), A. blicki (2n = 48, NFa = 62), A. abyssinicus (2n = 62, NFa = 64) and A. niloticus (2n = 62, NFa = 60–62). The taxonomic status of the remaining five cytotypes (A. cf. somalicus, 2n = 62 NFa = 62–63; ANI‐5, 2n = 56, NFa = 62; ANI‐6/6a 2n = 60, NFa = 72/76; ANI‐7, 2n = 56, NFa = 78; and ANI‐8, 2n = 44, NF = 72) is discussed. Finally, we reconstruct the phylogenetic relationships among all the known karyotypes on the basis of banding data available for the genus in Africa and show the occurrence of two main clades, each characterized by different types of chromosomal rearrangements. The times of the cladogenetic events, inferred by a molecular clock, indicate that karyotype evolution has accomplished almost all the dichotomic events from the end of the Miocene to the present day. The discovery of a large chromosomal differentiation between populations showing low genetic distances and intrapopulation chromosomal polymorphism suggests that the process of chromosomal differentiation in Arvicanthis is still ongoing and may possibly be responsible for speciation.     

Molecular phylogenetics of slit‐faced bats (Chiroptera: Nycteridae) reveal deeply divergent African lineages

The bat family Nycteridae contains only the genus Nycteris, which comprises 13 currently recognized species from Africa and the Arabian Peninsula, one species from Madagascar, and two species restricted to Malaysia and Indonesia in South‐East Asia. We investigated genetic variation, clade membership, and phylogenetic relationships in Nycteridae with broad sampling across Africa for most clades. We sequenced mitochondrial cytochrome b (cytb) and four independent nuclear introns (2,166 bp) from 253 individuals. Although our samples did not include all recognized species, we recovered at least 16 deeply divergent monophyletic lineages using independent mitochondrial and multilocus nuclear datasets in both gene tree and species tree analyses. Mean pairwise uncorrected genetic distances among species‐ranked Nycteris clades (17% for cytb and 4% for concatenated introns) suggest high levels of phylogenetic diversity in Nycteridae. We found a large number of designated clades whose members are distributed wholly or partly in East Africa (10 of 16 clades), indicating that Nycteris diversity has been historically underestimated and raising the possibility that additional unsampled and/or undescribed Nycteris species occur in more poorly sampled Central and West Africa. Well‐resolved mitochondrial, concatenated nuclear, and species trees strongly supported African ancestry for SE Asian species. Species tree analyses strongly support two deeply diverged subclades that have not previously been recognized, and these clades may warrant recognition as subgenera. Our analyses also strongly support four traditionally recognized species groups of Nycteris. Mitonuclear discordance regarding geographic population structure in Nycteris thebaica appears to result from male‐biased dispersal in this species. Our analyses, almost wholly based on museum voucher specimens, serve to identify species‐rank clades that can be tested with independent datasets, such as morphology, vocalizations, distributions, and ectoparasites. Our analyses highlight the need for a comprehensive revision of Nycteridae.     

Molecular phylogeny of the genus Helix (Pulmonata: Helicidae)

The vast diversity of land snail forms is insufficiently understood even in seemingly familiar taxa. This holds for Helix Linnaeus, 1758, a genus with several common edible species which comprises the largest Western Palearctic snails. The taxonomy of this genus, which has a centre of diversity in the eastern Mediterranean, has recently undergone significant changes, in both the delimitation of the genus itself and its species‐level systematics. Here, we compare the lineage diversity of Helix, as revealed by two mitochondrial markers, with the conclusions of the recently published morphology‐based taxonomic revision. For the molecular analysis, we assembled a representative data set covering almost all species of the genus as recognized by the mentioned revision. We obtained sequences not only from fresh and preserved soft tissues but also from dried tissue remains (some of them decades old) from shell collections. Our results show that the genus Helix, in the narrow sense proposed by recent studies, is paraphyletic because the genus Tacheopsis was unambiguously revealed as one of the tip branches of Helix. The monophyly of several species, as presently recognized, was not supported; partly, this may be attributed to a lineage diversity overlooked so far. This holds also for the type species of the genus, H. pomatia, which comprises at least one additional lineage. Greece, the Aegean and western Turkey is the core area for the diversity of Helix and its relatives, and the region is probably a major long‐term refuge for large Helicidae. The highest species diversity is found along the Alpide belt from the western Balkans to southern Turkey. The diversity of Helix in Europe, north of Greece and the Apennines, is a result of a single European radiation. Our data also suggest that past human activities likely influenced the present‐day distributions of some species.     

Cryptic diversity revealed in the leaf‐toed gecko Asaccus montanus (Squamata,Phyllodactylidae) from the Hajar Mountains of Arabia

Asaccus geckos are distributed in southwest Asia, mainly in Iran and Arabia. Currently, seven Asaccus species are recognized in Arabia, all endemic to the isolated Hajar Mountains in Oman and the UAE, an area regarded as a biodiversity and endemicity hotspot. Previous phylogenetic studies have shown a non‐monophyletic structure of the Arabian Asaccus species, with the Hajar endemic A. montanus diverging first from the remaining Iranian and Arabian taxa, thus suggesting a possible Arabian origin for the genus. Despite the species’ obvious phylogeographical importance, no study has yet explored its intraspecific diversity. In this study, we assessed the genetic diversity and phylogeography of A. montanus and its phylogenetic relationships with the rest of the Arabian Asaccus species and some available representatives from Iran. We used both mitochondrial and nuclear data to assess phylogenetic relationships based on haplotype networks, concatenated datasets and species trees, performed species delimitation analyses, and estimated divergence times and genetic diversity. We suggest Asaccus began diverging during the Middle Oligocene, a period of major tectonic activity in and around Arabia. Our results mainly support previous phylogenetic studies and uncover the presence of cryptic diversity within A. montanus. Asaccus montanus diverged in the Jebel Akhdar Mountain range into two deep allopatric lineages during the Late Pliocene. Our findings suggest further taxonomic research is necessary for this species, especially due to its vulnerable status and restricted range in an area of great conservation importance.     

Genetic diversity among African great apes based on mitochondrial DNA sequences

The mitochondrial DNA D-Loop region was sequenced, analyzed and used as a molecular marker for populations of chimpanzee (Pan troglodytes), bonobo (P. paniscus) and gorilla (Gorilla gorilla and G. beringei), and also compared with data previously reported for these taxa. In Gorilla, a main disjunction between western (G. gorilla) and eastern (G. beringei, including G. b. graueri) species was observed, as well as high mitochondrial diversity within the western species. The genetic distance values within G. gorilla (0.14) were higher than those between subspecies (eastern lowland and mountain 0.12). Likewise, values of genetic diversity within this species (0.05) were higher than those between species (western and eastern lowland gorilla 0.04). Similarly, in genus Pan a main differentiation between western (P. t. verus) and central forms (P. t. troglodytes and P. t. schweinfurthii) was observed. The obtained values of genetic distance and genetic diversity revealed that the central subspecies are closer to each other than either of them is to the western one, while bonobos composed a distinct clade that expresses a well-defined specific identity. The current distribution, phylogeny and levels of genetic diversity in African great ape populations are consistent with the hypothesis that Pleistocene climatic events led to cyclical periods of isolation in forest refugia followed by expansion and dispersal. The implications of this high level of genetic diversity for taxonomic classification, wildlife management and conservation are discussed.