Estimating the dwarfing rate of an extinct Sicilian elephant

A genetic glimpse of the Chinese straight-tusked elephants

Straight-tusked elephants (genus: Palaeoloxodon) including their island dwarf forms are extinct enigmatic members of the Pleistocene megafauna and the most common Pleistocene elephants after the mammoths. Their taxonomic placement has been revised several times. Using palaeogenomic evidence, previous studies suggested that the European P. antiquus has a hybrid origin, but no molecular data have been retrieved from their Asian counterparts, leaving a gap in our knowledge of the global phylogeography and population dynamics of Palaeoloxodon. Here, we captured a high-quality complete mitogenome from a Pleistocene Elephantidae molar (CADG841) from Northern China, which was previously morphologically assigned to the genus Elephas (Asian elephant), and partial mitochondrial sequences (838 bp) of another Palaeoloxodon sp. specimen (CADG1074) from Northeastern China. We found that both Chinese specimens cluster with a 244 000-year-old P. antiquus (specimen name: WE) from Western Europe, suggesting that this clade may represent a population with a large spatial span across Eurasia. Based on the fossil record and the molecular dating of both the divergences of different Palaeoloxodon mitochondrial clades and previously determined hybridization events, we propose that this Eurasian-wide WE clade provides evidence for an earlier migration and/or another hybridization event that happened in the evolutionary history of straight-tusked elephants.

A macroevolutionary pathway to megaherbivory

Several scenarios have been proposed to explain rapid net size increases in some early Cenozoic mammalian lineages: sustained and gradual directional change, successive occupation of adaptive zones associated with progressively larger body sizes, and nondirectional evolution associated with branching events in combination with higher diversification potential of the larger lineages. We test these hypotheses in brontotheres, which are among the first radiations of mammals that consistently evolved multitonne sizes. Body-mass evolution in brontotheres mainly occurred during speciation and had no preferential direction. Long-term directional change stemmed from the higher survival of larger lineages in less-saturated herbivore guilds. Our study emphasizes the role of differential species proliferation in explaining the long-term phenotypic trends observed in the fossil record, which are more than an accumulation of steady microevolutionary changes.

Fencing Can Alter Gene Flow of Asian Elephant Populations within Protected Areas

The Asian elephant is mostly confined to mountainous ranges and therefore risks population fragmentation if hard protected area (PA) boundaries near steep slopes prevent movement. We tested whether elephant gene flow is (i) controlled by slope and (ii) affected by the interplay between barriers and slope. We used 176 unique genotypes obtained non-invasively from fresh elephant dung to assess individual-by-individual genetic distance across the Western Ghats of India, a biodiversity hotspot. To assess landscape distance, 36 resistance models were produced by transforming a slope raster. Core areas and corridors were calculated from the raster that provided the best correlation between the genetic and distance matrices. The influence of the closure of PAs on gene flow was examined for one region, the Nilgiri Biosphere Reserve. The best resistance raster obtained by transforming the slope occupancy model was better than Euclidean distance for explaining genetic distance, indicating that slope partially controls gene flow. Fencing elephant PAs on hilly terrain reduces core areas and disrupts corridors. Consequently, hard PA boundaries abutting slopes can fragment elephant populations, but this can be ameliorated by protecting the adjacent flatter terrain.

Dating the Paleolithic: Trapped charge methods and amino acid geochronology

Despite the vast array of different geochronological tools available, dating the Paleolithic remains one of the discipline’s greatest challenges. This review focuses on two different dating approaches: trapped charge and amino acid geochronology. While differing in their fundamental principles, both exploit time-dependent changes in signals found within crystals to generate a chronology for the material dated and hence, the associated deposits. Within each method, there is a diverse range of signals that can be analyzed, each covering different time ranges, applicable to different materials and suitable for different paleoenvironmental and archaeological contexts. This multiplicity of signals can at first sight appear confusing, but it is a fundamental strength of the techniques, allowing internal checks for consistency and providing more information than simply a chronology. For each technique, we present an overview of the basis for the time-dependent signals and the types of material that can be analyzed, with examples of their archaeological application, as well as their future potential.

Paleogenomes Reveal a Complex Evolutionary History of Late Pleistocene Bison in Northeastern China

Steppe bison are a typical representative of the Mid-Late Pleistocene steppes of the northern hemisphere. Despite the abundance of fossil remains, many questions related to their genetic diversity, population structure and dispersal route are still elusive. Here, we present both near-complete and partial mitochondrial genomes, as well as a partial nuclear genome from fossil bison samples excavated from Late Pleistocene strata in northeastern China. Maximum-likelihood and Bayesian trees both suggest the bison clade are divided into three maternal haplogroups (A, B and C), and Chinese individuals fall in two of them. Bayesian analysis shows that the split between haplogroup C and the ancestor of haplogroups A and B dates at 326 ky BP (95% HPD: 397-264 ky BP). In addition, our nuclear phylogenomic tree also supports a basal position for the individual carrying haplogroup C. Admixture analyses suggest that CADG467 (haplogroup C) has a similar genetic structure to steppe bison from Siberia (haplogroup B). Our new findings indicate that the genetic diversity of Pleistocene bison was probably even higher than previously thought and that northeastern Chinese populations of several mammalian species, including Pleistocene bison, were genetically distinct.

[Small scale evolution]

Small-scale evolution or microevolution concerns evolution at the intra-specific level or between closely related species. At the intra-specific level, it allows the analysis of the evolutionary forces at work: mutation, genetic drift, migration and selection. Moreover, because of the short evolutionary time, it is easier to identify the genetic basis of observed phenotypic differences. Most studies focus on current populations but more and more analyses are performed on ancient DNA. This provides important information for tracing the history of populations and also allows the reconstruction of phenotypes of individuals that disappeared several thousand years ago. In this short review, I present studies showing how pre-zygotic or post-zygotic barriers involved in species formation are set up using the example of the geographical barrier due to the formation of the Isthmus of Panama and that of the heterochromatin divergence in Drosophilidae. I also describe the different approaches that have been used to identify the genetic basis of well known phenotypic variations: candidate gene approach (about melanism in felines), QTL mapping (variation in the number of lateral bone plates in sticklebacks), association study (pigmentation in the Asian ladybird). Finally, I illustrate the key impact of natural selection with the iconic example of the evolution of the beak of Galapagos finches, and the role of certain developmental genes in its morphological diversification.

Extreme Body Size Variation in Pleistocene Dwarf Elephants from the Siculo-Maltese Palaeoarchipelago: Disentangling the Causes in Time and Space

The phenomenon of insular dwarfism in proboscideans is particularly well represented on the Siculo-Maltese Palaeoarchipelago, an island group on which a species complex of palaeoloxodont elephants evolved during the Middle-Late Pleistocene. This likely included three species from Malta, four from Sicily (and possibly its palaeo-islands), and one from Favignana Island, ranging in size from the 1 m-tall Palaeoloxodon falconeri to continental-sized 4m-tall P. antiquus. However, our understanding of the causes for extreme differences in body size among insular samples in such a small geographic region is still limited. Here, I document the full range in size of elephants from the palaeoarchipelago, and discuss the reasons for size differences on the three islands in time and space in relation to predation, competition, resource limitation, accelerated life history, and duration of isolation. Differences in size between larger and smaller Sicilian elephants from Luparello Fissure, as well as possibly also in P. ex gr. P. mnaidriensis from Puntali Cave, San Teodoro Cave, and Favignana Island, may relate to the duration of isolation, or alternatively environmental stressors associated with the Last Glacial Maximum in the case of the Favignana elephant. Additionally, small but significant differences in size observable in Middle Pleistocene P. ex gr. P. falconeri from different localities on Sicily, as well as in Maltese P. ‘melitensis’ may also relate to duration of isolation, highlighting the need for better geochronological data in order to better distinguish macro-ecological causes driving body size change from more subtle effects relating to duration of isolation.