A New Species of Elephant-shrew (Afrotheria: Macroscelidea: Elephantulus) from South Africa

Reference quality genome sequence of Indian pomegranate cv. 'Bhagawa' (Punica granatum L.)

Pomegranate is an important fruit crop for ensuring livelihood and nutrition security in fragile semi-arid regions of the globe having limited irrigation resources. This is a high-value, nutritionally rich, and export-oriented agri-commodity that ensures high returns on investment to growers across the world. Although it is a valuable fruit crop, it has received only a limited genomics research outcome. To fast-track the pomegranate improvement program, de novo whole-genome sequencing of the main Indian cultivar 'Bhagawa' was initiated by the Indian Council of Agricultural Research-National Research Center on Pomegranate (ICAR-NRCP). We have demonstrated that a combination of commercially available technologies from Illumina, PacBio, 10X Genomics, and BioNano Genomics could be used efficiently for sequencing and reference-grade de novo assembly of the pomegranate genome. The research led to a final reference-quality genome assembly for 'Bhagawa' of 346.08 Mb in 342 scaffolds and an average N50 of 16.12 Mb and N90 of 1088.62 Kb. This assembly covered more than 98% of the estimated pomegranate genome size, 352.54 Mb. The LTR assembly index (LAI) value of 10 and 93.68% Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score over the 1,440 ortholog genes of the completed pomegranate genome indicates the quality of the assembled pomegranate genome. Furthermore, 29,435 gene models were discovered with a mean transcript length of 2,954 bp and a mean coding sequence length 1,090 bp. Four transcript data samples of pomegranate tissues were mapped over the assembled 'Bhagawa' genome up to 95% significant matches, indicating the high quality of the assembled genome. We have compared the 'Bhagawa' genome with the genomes of the pomegranate cultivars 'Dabenzi' and 'Taishanhong.' We have also performed whole-genome phylogenetic analysis using Computational Analysis of Gene Family Evolution (CAFE) and found that Eucalyptus grandis and pomegranate diverged 64 (60-70) million years ago. About 1,573 protein-coding resistance genes identified in the 'Bhagawa' genome were classified into 32 domains. In all, 314 copies of miRNA belonging to 26 different families were identified in the 'Bhagawa' genome. The reference-quality genome assembly of 'Bhagawa' is certainly a significant genomic resource for accelerated pomegranate improvement.

Occipital condyle width (OCW) is a highly accurate predictor of body mass in therian mammals

BACKGROUND

Body mass estimation is of paramount importance for paleobiological studies, as body size influences numerous other biological parameters. In mammals, body mass has been traditionally estimated using regression equations based on measurements of the dentition or limb bones, but for many species teeth are unreliable estimators of body mass and postcranial elements are unknown. This issue is exemplified in several groups of extinct mammals that have disproportionately large heads relative to their body size and for which postcranial remains are rare. In these taxa, previous authors have noted that the occiput is unusually small relative to the skull, suggesting that occiput dimensions may be a more accurate predictor of body mass.

RESULTS

The relationship between occipital condyle width (OCW) and body mass was tested using a large dataset (2127 specimens and 404 species) of mammals with associated in vivo body mass. OCW was found to be a strong predictor of body mass across therian mammals, with regression models of Mammalia as a whole producing error values (~ 31.1% error) comparable to within-order regression equations of other skeletal variables in previous studies. Some clades (e.g., monotremes, lagomorphs) exhibited specialized occiput morphology but followed the same allometric relationship as the majority of mammals. Compared to two traditional metrics of body mass estimation, skull length, and head-body length, OCW outperformed both in terms of model accuracy.

CONCLUSIONS

OCW-based regression models provide an alternative method of estimating body mass to traditional craniodental and postcranial metrics and are highly accurate despite the broad taxonomic scope of the dataset. Because OCW accurately predicts body mass in most therian mammals, it can be used to estimate body mass in taxa with no close living analogues without concerns of insufficient phylogenetic bracketing or extrapolating beyond the bounds of the data. This, in turn, provides a robust method for estimating body mass in groups for which body mass estimation has previously been problematic (e.g., "creodonts" and other extinct Paleogene mammals).

New records of a lost species and a geographic range expansion for sengis in the Horn of Africa

The Somali Sengi or Somali Elephant-shrew ('Elephantulus' revoilii, Macroscelidea, Mammalia) has been considered a "lost species" and is primarily known from about 39 museum specimens, with no new vouchered occurrence records since the early 1970s. The scientific literature contains no data concerning living Somali Sengi individuals and the species' current Data Deficient conservation status is attributable to an absence of modern information. Almost everything that has been published about the species is derived from anatomical examinations of historic specimens, gleaned from museum collection notes, or inferred from the known habits and ecology of other sengi taxa. Here we report new evidence that the Somali Sengi is currently extant. These data include voucher specimens, georeferenced occurrence localities, body measurements, habitat parameters, and DNA sequences. While the species is historically documented as endemic to Somalia, these new records are from the neighboring Republic of Djibouti and thus expand the Somali Sengi's known range in the Horn of Africa. Furthermore, Djiboutian locality data near international borders suggests that the Somali Sengi is also a current inhabitant of both Somalia and Ethiopia. Criteria that inform conservation status assessments (e.g., suitable habitat contiguity and occurrence in wildlife protected areas) can be positively characterized in Djibouti and therefore bode well for the survival of the Somali Sengi species. New data also inform previously undocumented substrate and sheltering affiliations. DNA analyses indicate that the Somali Sengi is a descendant of the Macroscelidini lineage and therefore reveal that the species' referral to the genus Elephantulus is incompatible with sengi phylogeny. This taxonomic issue is resolved by recognizing a new genus replacement and recombinant binomial that redesignates the Somali Sengi as Galegeeska revoilii (gen. nov., nov. comb). An analysis of ancestral biogeography suggests that the Somali Sengi has inhabited the Horn of Africa for more than 5.4 million years-and the recognition of the species' phylogenetic ancestry appends the already remarkable biogeographic story of the Macroscelidini tribe.

Spatial genetic structure in the rock hyrax (Procavia capensis) across the Namaqualand and western Fynbos areas of South Africa — a mitochondrial and microsatellite perspective

The interplay between biotic and abiotic environments is increasingly recognized as a major determinant of spatial genetic patterns. Among spatial genetic studies, saxicolous or rock-dwelling species remain underrepresented in spite of their strict dependence on landscape structure. Here we investigated patterns and processes operating at different spatial (fine and regional scales) and time scales (using mitochondrial and microsatellite markers) in the rock hyrax (Procavia capensis (Pallas, 1766)). Our focus was on the western seaboard of South Africa and included two recognized biodiversity hotspots (Cape Floristic Region and Succulent Karoo). At fine spatial scale, significant genetic structure was present between four rocky outcrops in an isolated population, likely driven by the social system of this species. At a broader spatial scale, ecological dependence on rocky habitat and population-level processes, in conjunction with landscape structure, appeared to be the main drivers of genetic diversity and structure. Large areas devoid of suitable rocky habitat (e.g., the Knersvlakte, Sandveld, and Cape Flats, South Africa) represent barriers to gene flow in the species, although genetic clusters closely follow climatic, geological, and phytogeographic regions, possibly indicating ecological specialization or adaptation as contributing factors enforcing isolation. Taken together, our study highlights the need to consider both intrinsic and extrinsic factors when investigating spatial genetic structures within species.

Phylogeography and niche modelling: reciprocal enlightenment

Phylogeography examines the spatial genetic structure of species. Environmental niche modelling (or ecological niche modelling; ENM) examines the environmental limits of a species’ ecological niche. These two fields have great potential to be used together. ENM can shed light on how phylogeographical patterns develop and help identify possible drivers of spatial structure that need to be further investigated. Specifically, ENM can be used to test for niche differentiation among clades, identify factors limiting individual clades and identify barriers and contact zones. It can also be used to test hypotheses regarding the effects of historical and future climate change on spatial genetic patterns by projecting niches using palaeoclimate or future climate data. Conversely, phylogeographical information can populate ENM with within-species genetic diversity. Where adaptive variation exists among clades within a species, modelling their niches separately can improve predictions of historical distribution patterns and future responses to climate change. Awareness of patterns of genetic diversity in niche modelling can also alert conservationists to the potential loss of genetically diverse areas in a species’ range. Here, we provide a simplistic overview of both fields, and focus on their potential for integration, encouraging researchers on both sides to take advantage of the opportunities available.

Evolutionary and ecological patterns within the South African Bathyergidae: Implications for taxonomy

The family Bathyergidae (comprising six genera) is a group of subterranean rodents endemic to sub-Saharan Africa. Our understanding of the evolution and species richness of the South African bathyergid genera Georychus, Bathyergus and Cryptomys is limited, with the majority of species listed as Least Concern by the IUCN Red List of Threatened Species. Genetic data suggest that several cryptic species may be present in these genera. To explore genetic and ecological distinctiveness, and evaluate taxonomic richness across the ranges of Georychus, Bathyergus and to a lesser degree, Cryptomys, as well as evaluate possible scenarios which have historically influenced evolutionary patterns, we employed four protein coding markers (one mitochondrial and three nuclear) along with distribution wide sampling schemes and large sample sizes. In addition, possible ecological differences among the different intra-generic clades were explored. Genera appear to have originated in the north-eastern interior of South Africa, following novel habitats created through the Post-African I erosion cycle and dramatic changes in climate and phytogeography. In each genus, multiple geographically discrete genetic lineages (clades) are supported by both the mitochondrial and nuclear data. These lineages bear signature of the fragmentation of wider historical distributions through major environmental changes since the middle Miocene (major uplift events, Post-African II erosion cycle, drainage evolution of major river systems, sea-level fluctuations as well as climatic changes and vegetation shifts), thereby leading to long-term isolation. Along with protracted periods of separation, it appears that ecological differences further delimit the lineages in relation to geology, phytogeographic preference, elevation, rainfall and temperature. As such, two lineages in Georychus (Clades 1 and 2) and one lineages in Cryptomys (Clade I) occur at higher elevations above the Great Escarpment (in older deposits harbouring grassland vegetation, with higher rainfall and lower daily temperatures), with the remaining lineages within these genera (Clades 3, 4 and 5 in Georychus and Clades III and IV in Cryptomys) occupying a low-land distribution with contrasting climatic and geological characteristics. Although significant differences in ecological variables were also observed between Bathyergus clades, these were not consistent, given their largely low-land distributions. Our results corroborate and expand previous suggestions that several cryptic species are present within the South African Bathyergidae.

Spatial genetic diversity in the Cape mole-rat, Georychus capensis: Extreme isolation of populations in a subterranean environment

The subterranean niche harbours animals with extreme adaptations. These adaptations decrease the vagility of taxa and, along with other behavioural adaptations, often result in isolated populations characterized by small effective population sizes, high inbreeding, population bottlenecks, genetic drift and consequently, high spatial genetic structure. Although information is available for some species, estimates of genetic diversity and whether this variation is spatially structured, is lacking for the Cape mole-rat (Georychus capensis). By adopting a range-wide sampling regime and employing two variable mitochondrial markers (cytochrome b and control region), we report on the effects that life-history, population demography and geographic barriers had in shaping genetic variation and population genetic patterns in G. capensis. We also compare our results to information available for the sister taxon of the study species, Bathyergus suillus. Our results show that Georychus capensis exhibits low genetic diversity relative to the concomitantly distributed B. suillus, most likely due to differences in habitat specificity, habitat fragmentation and historical population declines. In addition, the isolated nature of G. capensis populations and low levels of population connectivity has led to small effective population sizes and genetic differentiation, possibly aided by genetic drift. Not surprisingly therefore, G. capensis exhibits pronounced spatial structure across its range in South Africa. Along with geographic distance and demography, other factors shaping the genetic structure of G. capensis include the historical and contemporary impacts of mountains, rivers, sea-level fluctuations and elevation. Given the isolation and differentiation among G. capensis populations, the monotypic genus Georychus may represent a species complex.

Reconstructing the molecular phylogeny of giant sengis (Macroscelidea; Macroscelididae; Rhynchocyon)

Giant sengis (Macroscelidea; Macroscelididae; Rhynchocyon), also known as giant elephant-shrews, are small-bodied mammals that range from central through eastern Africa. Previous research on giant sengi systematics has relied primarily on pelage color and geographic distribution. Because some species have complex phenotypic variation and large geographic ranges, we used molecular markers to evaluate the phylogeny and taxonomy of the genus, which currently includes four species: R. chrysopygus, R. cirnei (six subspecies), R. petersi (two subspecies), and R. udzungwensis. We extracted DNA from fresh and historical museum samples from all taxa except one R. cirnei subspecies, and we generated and analyzed approximately 4700 aligned nucleotides (2685 bases of mitochondrial DNA and 2019 bases of nuclear DNA) to reconstruct a molecular phylogeny. We genetically evaluate Rhynchocyon spp. sequences previously published on GenBank, propose that the captive R. petersi population in North American zoos is likely R. p. adersi, and suggest that hybridization among taxa is not widespread in Rhynchocyon. The DNA sample we have from the distinctive but undescribed giant sengi from the Boni forest of northern coastal Kenya is unexpectedly nearly identical to R. chrysopygus, which will require further study. Our analyses support the current morphology-based taxonomy, with each recognized species forming a monophyletic clade, but we propose elevating R. c. stuhlmanni to a full species.

Home range and use of diurnal shelters by the Etendeka round-eared sengi, a newly discovered Namibian endemic desert mammal

To understand habitat use by the newly described Etendeka round-eared sengi (Macroscelides micus) in northwestern Namibia, we radio-tracked five individuals for nearly a month. Home ranges (100% convex polygons) in the rocky desert habitat were remarkably large (mean 14.9 ha) when compared to sengi species in more mesic habitats (<1.5 ha). The activity pattern of M. micus was strictly nocturnal, which contrasts to the normal diurnal or crepuscular activity of other sengis. The day shelters of M. micus were under single rocks and they likely were occupied by single sengis. One tagged sengi used 22 different day shelters during the study. On average, only 7% of the day shelters were used more than once by the five tagged sengis. The shelters were also unusual for a small mammal in that they were unmodified in terms of excavation or nesting material. Shelter entrances were significantly oriented to face south by south west (average 193°), away from the angle of the prevailing midday sun. This suggests that solar radiation is probably an important aspect of M. micus thermal ecology, similar to other sengis. Compared to published data on other sengis, M. micus generally conforms to the unique sengi adaptive syndrome, but with modifications related to its hyper-arid habitat.

A phylogeographic survey of the pygmy mouse Mus minutoides in South Africa: taxonomic and karyotypic inference from cytochrome b sequences of museum specimens

The African pygmy mice (Mus, subgenus Nannomys) are a group of small-sized rodents that occur widely throughout sub-Saharan Africa. Chromosomal diversity within this group is extensive and numerous studies have shown the karyotype to be a useful taxonomic marker. This is pertinent to Mus minutoides populations in South Africa where two different cytotypes (2n = 34, 2n = 18) and a modification of the sex determination system (due to the presence of a Y chromosome in some females) have been recorded. This chromosomal diversity is mirrored by mitochondrial DNA sequences that unambiguously discriminate among the various pygmy mouse species and, importantly, the different M. minutoides cytotypes. However, the geographic delimitation and taxonomy of pygmy mice populations in South Africa is poorly understood. To address this, tissue samples of M. minutoides were taken and analysed from specimens housed in six South African museum collections. Partial cytochrome b sequences (400 pb) were successfully amplified from 44% of the 154 samples processed. Two species were identified: M. indutus and M. minutoides. The sequences of the M. indutus samples provided two unexpected features: i) nuclear copies of the cytochrome b gene were detected in many specimens, and ii) the range of this species was found to extend considerably further south than is presently understood. The phylogenetic analysis of the M. minutoides samples revealed two well-supported clades: a Southern clade which included the two chromosomal groups previously identified in South Africa, and an Eastern clade that extended from Eastern Africa into South Africa. Congruent molecular phylogenetic and chromosomal datasets permitted the tentative chromosomal assignments of museum specimens within the different clades as well as the correction of misidentified museum specimens.

Brain volume of the newly-discovered species Rhynchocyon udzungwensis (Mammalia: Afrotheria: Macroscelidea): implications for encephalization in sengis

The Gray-faced Sengi (Rhynchocyon udzungwensis) is a newly-discovered species of sengi (elephant-shrew) and is the largest known extant representative of the order Macroscelidea. The discovery of R. udzungwensis provides an opportunity to investigate the scaling relationship between brain size and body size within Macroscelidea, and to compare this allometry among insectivorous species of Afrotheria and other eutherian insectivores. We performed a spin-echo magnetic resonance imaging (MRI) scan on a preserved adult specimen of R. udzungwensis using a 7-Tesla high-field MR imaging system. The brain was manually segmented and its volume was compiled into a dataset containing previously-published allometric data on 56 other species of insectivore-grade mammals including representatives of Afrotheria, Soricomorpha and Erinaceomorpha. Results of log-linear regression indicate that R. udzungwensis exhibits a brain size that is consistent with the allometric trend described by other members of its order. Inter-specific comparisons indicate that macroscelideans as a group have relatively large brains when compared with similarly-sized terrestrial mammals that also share a similar diet. This high degree of encephalization within sengis remains robust whether sengis are compared with closely-related insectivorous afrotheres, or with more-distantly-related insectivorous laurasiatheres.

Abiotic and biotic determinants of tick burdens in the eastern rock sengi (Elephantulus myurus)

Ticks are important vectors of pathogens of medical and veterinary importance worldwide. In spite of their economic importance, our current knowledge about the factors affecting tick prevalence and abundance in tropical and subtropical regions is rather limited. Both abiotic (e.g. temperature) as well as biotic variables (e.g. host sex) have been identified as key determinants of distributions. Eastern rock sengis or elephant shrews (Elephantulus myurus, Macroscelidea: Cacroscelididae, Thomas & Schwann) are widely distributed throughout Africa and can harbour a large number of tick species and substantial tick burdens. In the present study, we evaluated the contribution of climate and host factors on tick burdens of sengis. Throughout the year sengis carried high abundances of immature stages of a single tick species, Rhipicephalus sp. near warburtoni. There was no evidence that host parameters affected tick burdens. However, larval abundance decreased with increasing ambient temperatures and both larvae and nymphs were negatively affected by rainfall 2 months before the sampling month. In addition, nymphal burdens decreased with increasing minimum temperatures. Our results suggest that climate factors are the largest constraint for the immature stages of R. sp. near warburtoni and that eastern rock sengis could play a crucial role in the dynamics of tick-borne diseases as a result of the large tick burdens they can sustain.

The chromosomes of Afrotheria and their bearing on mammalian genome evolution

Afrotheria is the clade of placental mammals that, together with Xenarthra, Euarchontoglires and Laurasiatheria, represents 1 of the 4 main recognized supraordinal eutherian clades. It reunites 6 orders of African origin: Proboscidea, Sirenia, Hyracoidea, Macroscelidea, Afrosoricida and Tubulidentata. The apparently unlikely relationship among such disparate morphological taxa and their possible basal position at the base of the eutherian phylogenetic tree led to a great deal of attention and research on the group. The use of biomolecular data was pivotal in Afrotheria studies, as they were the basis for the recognition of this clade. Although morphological evidence is still scarce, a plethora of molecular data firmly attests to the phylogenetic relationship among these mammals of African origin. Modern cytogenetic techniques also gave a significant contribution to the study of Afrotheria, revealing chromosome signatures for the group as a whole, as well as for some of its internal relationships. The associations of human chromosomes HSA1/19 and 5/21 were found to be chromosome signatures for the group and provided further support for Afrotheria. Additional chromosome synapomorphies were also identified linking elephants and manatees in Tethytheria (the associations HSA2/3, 3/13, 8/22, 18/19 and the lack of HSA4/8) and elephant shrews with the aardvark (HSA2/8, 3/20 and 10/17). Herein, we review the current knowledge on Afrotheria chromosomes and genome evolution. The already available data on the group suggests that further work on this apparently bizarre assemblage of mammals will provide important data to a better understanding on mammalian genome evolution.

Phylogeny and taxonomy of the round-eared sengis or elephant-shrews, genus Macroscelides (Mammalia, Afrotheria, Macroscelidea)

The round-eared sengis or elephant-shrews (genus Macroscelides) exhibit striking pelage variation throughout their ranges. Over ten taxonomic names have been proposed to describe this variation, but currently only two taxa are recognized (M. proboscideus proboscideus and M. p. flavicaudatus). Here, we review the taxonomic history of Macroscelides, and we use data on the geographic distribution, morphology, and mitochondrial DNA sequence to evaluate the current taxonomy. Our data support only two taxa that correspond to the currently recognized subspecies M. p. proboscideus and M. p. flavicaudatus. Mitochondrial haplotypes of these two taxa are reciprocally monophyletic with over 13% uncorrected sequence divergence between them. PCA analysis of 14 morphological characters (mostly cranial) grouped the two taxa into non-overlapping clusters, and body mass alone is a relatively reliable distinguishing character throughout much of Macroscelides range. Although fieldworkers were unable to find sympatric populations, the two taxa were found within 50 km of each other, and genetic analysis showed no evidence of gene flow. Based upon corroborating genetic data, morphological data, near sympatry with no evidence of gene flow, and differences in habitat use, we elevate these two forms to full species.

Morphological cranial diversity contributes to phylogeny in soft-furred sengis (Afrotheria, Macroscelidea)

Despite the well-supported Macroscelidea phylogeny proposed at the end of the 1960s, several systematic arrangements have been suggested in the last 20 years, raising doubts about the phylogeny of the Macroscelidinae; sengi inter-specific relationships are still debated to this day. The main issue of concern involves the supposed Elephantulus diphyly. To solve this persisting debate about sengi phylogeny, we examined the cranium ventral surface of 13 species using geometric morphometric techniques and neighbour-joining algorithms. This study supported the idea that the ventral side of the sengi cranium has the potential to provide important signals for reconstructing the Macroscelidea phylogeny. The phylogenetic signals seemed to differentiate between two major clades in the sengi radiation. In the first clade, the two monospecific genera (Petrodromus and Macroscelides), the two African Horn species (Elephantulus revoilii and E. rufescens), and the only North African species (E. rozeti) were clustered together. The second clade includes the remnant south-central African Elephantulus species. Our results were in agreement with both mitochondrial and nuclear data, confirmed that there is no Elephantulus monophyly and highlighted the close relationship between Petrodromus and E. rozeti. It appears that all the soft-furred sengi species are organised in two evolutionary lines: an old monophyletic clade, comprising only Elephantulus species, and a new polyphyletic clade, including P. tetradactylus, M. proboscideus, and E. rozeti. This requires a taxonomic and nomenclatural rearrangement within Macroscelidinae, where the phylogenetic position of the remnant 4 (of 12) Elephantulus species has yet to be fully defined.