Phylogeny and conservation priorities of afrotherian mammals (Afrotheria,Mammalia)

Kuntner, M., May‐Collado, L. J. & Agnarsson, I. (2010). Phylogeny and conservation priorities of afrotherian mammals (Afrotheria, Mammalia). —Zoologica Scripta, 40, 1–15. Phylogenies play an increasingly important role in conservation biology providing a species‐specific measure of biodiversity – evolutionary distinctiveness (ED) or phylogenetic diversity (PD) – that can help prioritize conservation effort. Currently, there are many available methods to integrate phylogeny and extinction risk, with an ongoing debate on which may be best. However, the main constraint on employing any of these methods to establish conservation priorities is the lack of detailed species‐level phylogenies. Afrotheria is a recently recognized clade grouping anatomically and biologically diverse placental mammals: elephants and mammoths, dugong and manatees, hyraxes, tenrecs, golden moles, elephant shrews and aardvark. To date, phylogenetic studies have focused on understanding higher level relationships among the major groups within Afrotheria. Here, we provide a species‐level phylogeny of Afrotheria based on nine molecular loci, placing nearly 70% of the extant afrotherian species (50) and five extinct species. We then use this phylogeny to assess conservation priorities focusing on the widely used evolutionary distinctiveness and global endangeredness (EDGE) method and how that compares to the more recently developed PD framework. Our results support the monophyly of Afrotheria and its sister relationship to Xenarthra. Within Afrotheria, the basal division into Afroinsectiphilia (aardvark, tenrecs, golden moles and elephant shrews) and Paenungulata (hyraxes, dugongs, manatees and elephants) is supported, as is the monophyly of all afrotherian families: Elephantidae, Procaviidae, Macroscelididae, Chrysochloridae, Tenrecidae, Trichechidae and Dugongidae. Within Afroinsectiphilia, we recover the most commonly proposed topology (Tubulidentata sister to Afroscoricida plus Macroscelidea). Within Paenungulata, Sirenia is sister to Hyracoidea plus Proboscidea, a controversial relationship supported by morphology. Within Proboscidea, the mastodon is sister to the remaining elephants and the woolly mammoth sister to the Asian elephant, while both living elephant genera, Loxodonta and Elephas are paraphyletic. Top ranking evolutionarily unique species always included the aardvark, followed by several species of elephant shrews and tenrecs. For conservation priorities top ranking species always included the semi‐aquatic Nimba otter shrew, some poorly known species, such as the Northern shrew tenrec, web‐footed tenrec, giant otter shrew and Giant golden mole, as well as high profile conservation icons like Asian elephant, dugong and the three species of manatee. Conservation priority analyses were broadly congruent between the EDGE and PD methodologies. However, for certain species EDGE overestimates conservation urgency as it, unlike PD, fails to account for the status of closely related, but less threatened, species. Therefore, PD offers a better guide to conservation decisions.     

A phylogenetic estimate for golden moles (Mammalia,Afrotheria, Chrysochloridae)

Background  

Golden moles (Chrysochloridae) are small, subterranean, afrotherian mammals from South Africa and neighboring regions. Of the 21 species now recognized, some (e.g., Chrysochloris asiatica, Amblysomus hottentotus) are relatively common, whereas others (e.g., species of Chrysospalax, Cryptochloris, Neamblysomus) are rare and endangered. Here, we use a combined analysis of partial sequences of the nuclear GHR gene and morphological characters to derive a phylogeny of species in the family Chrysochloridae.     

Petrosal and Bony Labyrinth Morphology Supports Paraphyly of Elephantulus Within Macroscelididae (Mammalia,Afrotheria)

Interest in the phylogeny of Macroscelididae (sengis or elephant shrews) has been prompted by molecular studies indicating that Elephantulus rozeti is best placed as the sister group of Petrodromus tetradactylus (this clade being in turn the sister taxon to Macroscelides proboscideus) than among other species of the genus Elephantulus. Until now, no discrete morphological characters have been proposed to support the grouping of E. rozeti, Petrodromus, and Macroscelides into this single so-called ‘Panelephantulus’ clade. Here, we employed μCT scanning in order to investigate the petrosal and bony labyrinth (bony capsule of the inner ear) morphology of most species of extant Macroscelididae. We performed a cladistic analysis on ear traits and found that despite some convergences (e.g., concerning the bony arterial canals in Macroscelides and Rhynchocyon) the middle and inner ear morphology furnishes significant support for the ‘Panelephantulus’ clade. In our analysis, this clade is unambigously supported by the presence of a fully ossified stapediofacial tube. Two additional characters (the presence of a bony septum at the mouth of the fenestra cochleae dividing the D3 sinus into two distinct cavities and the absence of an accessory lateral pneumatic fossa) could also support ‘Panelephantulus.’ These newly discovered morphological characters support the molecular phylogenies published and highlight the importance of coding hitherto difficult to sample morphologies within cladistic analyses using micro-CT techniques. Taxonomic implications are briefly discussed.     

Homoplasy in the ear region of Tethytheria and the systematic position of Embrithopoda (Mammalia,Afrotheria)

The ear region of mammals has long been considered as morphologically very conservative and accordingly, phylogenetically useful. In this study, the anatomy of the petrosal and bony labyrinth (osseous inner ear) of Numidotherium (Proboscidea) and Arsinoitherium (Embrithopoda) are investigated and compared in order to assess the evolution of ear region characters in proboscideans and embrithopods. Using a cladistic analysis across Paenungulata based on ear region characters only, we found that Arsinoitherium is surprisingly best placed as a crown proboscideans to the exclusion of Numidotherium and Phosphatherium, which results in the paraphyly of proboscidean. The clade Proboscidea is actually well supported by dental and post-cranial characters, and we propose that this result underlines the great amount of morphological convergences in the ear region of Embrithopoda and Proboscidea, possibly due to convergent evolution of capabilities toward infrasonic hearing.     

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.     

Chromosome painting among Proboscidea, Hyracoidea and Sirenia: support for Paenungulata (Afrotheria, Mammalia) but not Tethytheria

Despite marked improvements in the interpretation of systematic relationships within Eutheria, particular nodes, including Paenungulata (Hyracoidea, Sirenia and Proboscidea), remain ambiguous. The combination of a rapid radiation, a deep divergence and an extensive morphological diversification has resulted in a limited phylogenetic signal confounding resolution within this clade both at the morphological and nucleotide levels. Cross-species chromosome painting was used to delineate regions of homology between Loxodonta africana (2n=56), Procavia capensis (2n=54), Trichechus manatus latirostris (2n=48) and an outgroup taxon, the aardvark (Orycteropus afer, 2n=20). Changes specific to each lineage were identified and although the presence of a minimum of 11 synapomorphies confirmed the monophyly of Paenungulata, no change characterizing intrapaenungulate relationships was evident. The reconstruction of an ancestral paenungulate karyotype and the estimation of rates of chromosomal evolution indicate a reduced rate of genomic repatterning following the paenungulate radiation. In comparison to data available for other mammalian taxa, the paenungulate rate of chromosomal evolution is slow to moderate. As a consequence, the absence of a chromosomal character uniting two paenungulates (at the level of resolution characterized in this study) may be due to a reduced rate of chromosomal change relative to the length of time separating successive divergence events.     

Why is there discordant diversity in sengi (Mammalia: Afrotheria: Macroscelidea) taxonomy and ecology?

The seventeen species of sengis or elephant-shrews form a well-defined clade of mammals endemic to Africa that occupy the extremes of terrestrial habitats, from coastal deserts to montane forests. Because of their isolation on Africa soon after the break-up of Gondwanaland, theoretically sengis initially evolved with little competition from other placental radiations. Their life history features include myrmecophagy, saltatorial gaits, no or limited use of nests, social monogamy, small litters of precocial young and absentee maternal care of neonates. These traits together are unique to the Macroscelidea and represent a wedding of features usually associated with either small antelopes or anteaters. Combined, these features define an adaptive syndrome that presumably has been relatively immune to competition from contemporary mammals, partially due to phylogenetic inertia. Yet paradoxically, the syndrome is well suited to a wide range of terrestrial habitats, resulting in low taxonomic diversity. Because of their unusual phylogeny and low species diversity, conservation interest is high for those sengis with relatively low densities in fragmented forests.     

Size, Speed and Buoyancy Adaptations in Aquatic Animals

Animals are denser than either fresh water or sea water, andtherefore tend to sink, unless they have adaptations that givebuoyancy. Very small organisms sink slowly, reproduce rapidlyand can be kept suspended by natural turbulence: individualslost by sinking are replaced by reproduction. This is likelyto be effective only for organisms of less than 150µmdiameter. Larger animals will sink unless they swim or evolvebuoyancy organs. Hovering is one of the options available tothem, but the "hop and sink" technique used by some copepodsis more economical than steady hovering. Another option is touse fins as hydrofoils, as sharks, tunnies and many squids do.This implies an energy cost because work has to be done againstdrag on the hydrofoils. Many animals are made buoyant by gas-filledfloats, low-density organic compounds or body fluids of unusualionic composition. Such buoyancy aids increase the energy costof swimming at given speed because they increase the animal'sbulk. Buoyancy aids are more economical than hydrofoils foranimals that swim slowly but hydrofoils are more economicalfor those that swim fast.     

New remains of Chambius kasserinensis from the Eocene of Tunisia and evaluation of proposed affinities for Macroscelidea (Mammalia,Afrotheria)

Abstract

Chambius kasserinensis from the late Early or early Middle Eocene Chambi locality, central Tunisia, is undoubtedly the oldest known macroscelidid and possibly the basalmost representative of the order Macroscelidea. Hence, since its discovery in 1986, Chambius has played a key role in analyses focusing on afrotherian and eutherian phylogeny; for instance, as early as 1995, Butler’s review of fossil macroscelideans highlighted the central position of Chambius in the origin of the order. Despite this, Chambius remained poorly known until recently. Here based on new mandibular fragments, well-preserved upper molars and CT scan analysis of the holotype maxilla, Chambius is revised. Its dentition is first described in detail, providing a precise characterization of the genus. Chambius is notably defined by a submolariform P₄ with a three-cusped talonid, a reduced talonid on M₂, and a prominent metaconule on M^1?2. Interestingly, the two transverse lophs of the upper molars are basically formed by preconulecristae, evoking the recently defined peculiar bilophodonty of paenungulates. Comparisons with other Paleogene and modern macroscelidids, European Louisinidae, and North American Apheliscidae are also made, allowing the various hypotheses about the origin and early evolution of macroscelidids to be reviewed.     

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.     

Les Lagomerycidae (Artiodactyla, Mammalia) de FranceThe French Lagomerycidae (Cervoidea, Artiodactyla, Mammalia)

The Lagomerycidae, a small family of the Cervoidea, is known in France by the genera Lagomeryx, Ligeromeryx and Stephanocemas. Lagomeryx contains three species, the other two genera one species only. This family is known from MN3 to MN5.     

A New Late Miocene Odobenid (Mammalia: Carnivora) from Hokkaido,Japan Suggests Rapid Diversification of Basal Miocene Odobenids

The modern walrus, Odobenus rosmarus, is specialized and only extant member of the family Odobenidae. They were much more diversified in the past, and at least 16 genera and 20 species of fossil walruses have been known. Although their diversity increased in the late Miocene and Pliocene (around 8–2 Million years ago), older records are poorly known. A new genus and species of archaic odobenid, Archaeodobenus akamatsui, gen. et sp. nov. from the late Miocene (ca. 10.0–9.5 Ma) top of the Ichibangawa Formation, Hokkaido, northern Japan, suggests rapid diversification of basal Miocene walruses. Archaeodobenus akamatsui is the contemporaneous Pseudotaria muramotoi from the same formation, but they are distinguishable from each other in size and shape of the occipital condyle, foramen magnum and mastoid process of the cranium, and other postcranial features. Based on our phylogenetic analysis, A. akamatsui might have split from P. muramotoi at the late Miocene in the western North Pacific. This rapid diversification of the archaic odobenids occurred with a combination of marine regression and transgression, which provided geological isolation among the common ancestors of extinct odobenids.     

Comparative Anatomy of the Petrosal Bone of Dichobunoids,Early Members of Artiodactylamorpha (Mammalia)

Among Artiodactylamorpha, dichobunoids are some of the oldest fossil species that have been associated with Artiodactyla, the crown clade that includes hippopotamids, camelids, suoids, ruminants, and cetaceans. These important fossil species are known from early Eocene rocks of North America, Europe, and Asia, but their phylogenetic position has yet to be well resolved. Before generating such a phylogeny, it is first critical to document all of the anatomy of known dichobunoid fossils. Here we use CT scans to describe previously undescribed anatomy of the petrosal bone, a complex part of the mammalian skull that contains many variable and phylogenetically informative features. Results show that these extinct species share a number of features that are not documented in modern species including a lateral process of the epitympanic wing constituting the medial border of the piriform fenestra, and a tegmen tympani foramen that may have given passage to the ramus superior of the stapedial artery. Future comprehensive phylogenetic studies may show that many of these characters are plesiomophic for Artiodactylamopha. Some species (Diacodexis, Homacodon and ?Helohyus) exhibit a dorsolateral exposure of the mastoid region of the petrosal on the temporal part of the cranium. This uncommon feature has, to our knowledge, not been reported in another euungulate group.     

What Lies Beneath: Sub-Articular Long Bone Shape Scaling in Eutherian Mammals and Saurischian Dinosaurs Suggests Different Locomotor Adaptations for Gigantism

Eutherian mammals and saurischian dinosaurs both evolved lineages of huge terrestrial herbivores. Although significantly more saurischian dinosaurs were giants than eutherians, the long bones of both taxa scale similarly and suggest that locomotion was dynamically similar. However, articular cartilage is thin in eutherian mammals but thick in saurischian dinosaurs, differences that could have contributed to, or limited, how frequently gigantism evolved. Therefore, we tested the hypothesis that sub-articular bone, which supports the articular cartilage, changes shape in different ways between terrestrial mammals and dinosaurs with increasing size. Our sample consisted of giant mammal and reptile taxa (i.e., elephants, rhinos, sauropods) plus erect and non-erect outgroups with thin and thick articular cartilage. Our results show that eutherian mammal sub-articular shape becomes narrow with well-defined surface features as size increases. In contrast, this region in saurischian dinosaurs expands and remains gently convex with increasing size. Similar trends were observed in non-erect outgroup taxa (monotremes, alligators), showing that the trends we report are posture-independent. These differences support our hypothesis that sub-articular shape scales differently between eutherian mammals and saurischian dinosaurs. Our results show that articular cartilage thickness and sub-articular shape are correlated. In mammals, joints become ever more congruent and thinner with increasing size, whereas archosaur joints remained both congruent and thick, especially in sauropods. We suggest that gigantism occurs less frequently in mammals, in part, because joints composed of thin articular cartilage can only become so congruent before stress cannot be effectively alleviated. In contrast, frequent gigantism in saurischian dinosaurs may be explained, in part, by joints with thick articular cartilage that can deform across large areas with increasing load.     

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.     

Humerus development in moles (Talpidae,Mammalia)

The humerus of fossorial moles has a highly derived anatomy, reflecting the ecological specialization of these animals for digging. It is short and broad, with enlarged muscle attachment sites and pronounced articulations compared to non‐fossorial sister taxa and other mammals. Both condyles are rotated in opposite directions, resulting in a torsion which is unique among eutherian mammals. The development of this exceptional bone was studied in embryonic stages of the fossorial Iberian mole (Talpa occidentalis) from mesenchymal condensation to incipient ossification based on histological serial sections using 3D reconstruction methods. For comparison, embryonic stages of the semi‐fossorial Japanese shrew mole (Urotrichus talpoides) as well as a sister taxon of moles, the terrestrial North American least shrew (Cryptotis parva), were studied. Results show that the humerus of Talpa already shows its derived anatomy with broadened muscle attachment sites and distinct articulations at early cartilaginous stages, when ossification has just started in the mid‐diaphyseal region. The torsion takes place simultaneously with the medial rotation of the forelimbs. The supracondylar foramen is closed in all studied Talpa embryos, but patent in Cryptotis and Urotrichus. This is an example of developmental penetrance, suggesting that variation of adult elements can be found at early stages as well.     

Dental Ontogeny in Macroscelides proboscideus (Afrotheria) and Erinaceus europaeus (Lipotyphla)

We investigated the state of dental eruption in specimens of Macroscelides proboscideus and Erinaceus europaeus of known age. When M. proboscideus reaches adult size and sexual maturity, few or none of its replaced permanent cheek teeth have erupted. The approximate sequence of upper tooth eruption is P1, [I3, C, M1], [I1–2], M2, P4, [P2, P3]. Chronologically, E. europaeus erupts its molars and most premolars prior to M. proboscideus; but its first two upper incisors erupt after those of M. proboscideus, and its canines erupt around the same time. The approximate sequence of upper tooth eruption in E. europaeus is [M1, M2, P2, I3], C, M3, P4, P3, I2, I1. Unlike M. proboscideus, E. europaeus does not reach adult size until all permanent teeth except for the anterior incisors have erupted. While not unique among mammals, the attainment of adult body size prior to complete eruption of the permanent cheek teeth is particularly common among macroscelidids and other afrotherians.     

Contemporary Parallel Diversification,Antipredator Adaptations and Phenotypic Integration in an Aquatic Isopod

It is increasingly being recognized that predation can be a strong diversifying agent promoting ecological divergence. Adaptations against different predatory regimes can emerge over short periods of time and include many different traits. We studied antipredator adaptations in two ecotypes of an isopod (Asellus aquaticus) that have, diverged in parallel in two Swedish lakes over the last two decades. We quantified differences in escape speed, morphology and behavior for isopods from different ecotypes present in these lakes. Isopods from the source habitat (reed) coexist with mainly invertebrate predators. They are more stream-profiled and have higher escape speeds than isopods in the newly colonized stonewort habitat, which has higher density of fish predators. Stonewort isopods also show more cautious behaviors and had higher levels of phenotypic integration between coloration and morphological traits than the reed isopods. Colonization of a novel habitat with a different predation regime has thus strengthened the correlations between pigmentation and morphology and weakened escape performance. The strong signature of parallelism for these phenotypic traits indicates that divergence is likely to be adaptive and is likely to have been driven by differences in predatory regimes. Furthermore, our results indicate that physical performance, behavior and morphology can change rapidly and in concert as new habitats are colonized.