Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant, “subfossil” koala lemur Megaladapis edwardsi

No endemic Madagascar animal with body mass >10 kg survived a relatively recent wave of extinction on the island. From morphological and isotopic analyses of skeletal “subfossil” remains we can reconstruct some of the biology and behavioral ecology of giant lemurs (primates; up to ∼160 kg) and other extraordinary Malagasy megafauna that survived into the past millennium. Yet, much about the evolutionary biology of these now-extinct species remains unknown, along with persistent phylogenetic uncertainty in some cases. Thankfully, despite the challenges of DNA preservation in tropical and subtropical environments, technical advances have enabled the recovery of ancient DNA from some Malagasy subfossil specimens. Here, we present a nuclear genome sequence (∼2× coverage) for one of the largest extinct lemurs, the koala lemur Megaladapis edwardsi (∼85 kg). To support the testing of key phylogenetic and evolutionary hypotheses, we also generated high-coverage nuclear genomes for two extant lemurs, Eulemur rufifrons and Lepilemur mustelinus, and we aligned these sequences with previously published genomes for three other extant lemurs and 47 nonlemur vertebrates. Our phylogenetic results confirm that Megaladapis is most closely related to the extant Lemuridae (typified in our analysis by E. rufifrons) to the exclusion of L. mustelinus, which contradicts morphology-based phylogenies. Our evolutionary analyses identified significant convergent evolution between M. edwardsi and an extant folivore (a colobine monkey) and an herbivore (horse) in genes encoding proteins that function in plant toxin biodegradation and nutrient absorption. These results suggest that koala lemurs were highly adapted to a leaf-based diet, which may also explain their convergent craniodental morphology with the small-bodied folivore Lepilemur.

The use of malacological analysis in studies on anthropogenic transformations in microhabitats: an example from the Cracow region, southern Poland

The presented study is dedicated to the assessment of the scope and degree of anthropopressure, and the dependence of its intensity on the characteristics and nature of micro-environments. The research was based on the subfossil remains of molluscs. Eleven profiles of Late Holocene sediments in the Dulówka valley near Cracow were subjected to malacological analysis. In the upper part of the valley, there are calcareous tufas containing rich molluscan assemblages with a large share of shade-loving species. In the lower part, malacofauna dominated by open-country snails occurs in fluvial sediments. Radiocarbon dating has shown that mollusc-bearing deposits represent the last 2,000 years. The diversity of ecological features of molluscan assemblages in different parts of the valley depends on the intensity of anthropopressure. In the upper part, natural forest communities have survived to the present day, and anthropopressure has only been marked to a limited extent. The lower section has undergone a major transformation, mainly due to deforestation and the development of agricultural areas. Unfavorable terrain conditions for the human economy should be considered the major cause of the low anthropopressure intensity in the upper part of the valley. The malacological analysis used in the study allowed showing a significant diversity of microhabitats within the valley and its uneven susceptibility to human interference in natural processes.

Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant ‘subfossil’ koala lemur Megaladapis edwardsi

No endemic Madagascar animal with body mass >10 kg survived a relatively recent wave of extinction on the island. From morphological and isotopic analyses of skeletal ‘subfossil’ remains we can reconstruct some of the biology and behavioral ecology of giant lemurs (primates; up to ~160 kg), elephant birds (up to ~860 kg), and other extraordinary Malagasy megafauna that survived well into the past millennium. Yet much about the evolutionary biology of these now extinct species remains unknown, along with persistent phylogenetic uncertainty in some cases. Thankfully, despite the challenges of DNA preservation in tropical and sub-tropical environments, technical advances have enabled the recovery of ancient DNA from some Malagasy subfossil specimens. Here we present a nuclear genome sequence (~2X coverage) for one of the largest extinct lemurs, the koala lemur Megaladapis edwardsi (~85kg). To support the testing of key phylogenetic and evolutionary hypotheses we also generated new high-coverage complete nuclear genomes for two extant lemur species, Eulemur rufifrons and Lepilemur mustelinus, and we aligned these sequences with previously published genomes for three other extant lemur species and 47 non-lemur vertebrates. Our phylogenetic results confirm that Megaladapis is most closely related to the extant Lemuridae (typified in our analysis by E. rufifrons) to the exclusion of L. mustelinus, which contradicts morphology-based phylogenies. Our evolutionary analyses identified significant convergent evolution between M. edwardsi and extant folivorous primates (colobine monkeys) and ungulate herbivores (horses) in genes encoding protein products that function in the biodegradation of plant toxins and nutrient absorption. These results suggest that koala lemurs were highly adapted to a leaf-based diet, which may also explain their convergent craniodental morphology with the small-bodied folivore Lepilemur.

Effect of Temperature on the Size of Sedimentary Remains of Littoral Chydorids

The body size of aquatic invertebrates is, to a great extent, dependent on ambient temperature, but size distributions are also determined by other factors like food supply and predation. The effect of temperature on organisms is formulated in the temperature–size hypothesis, which predicts a smaller body size with increasing temperature. In this study, the effect of temperature on the subfossil remains of three littoral Cladocera (Alona affnis, A. quadrangularis, and Chydorus cf. sphaericus) was investigated. Exoskeletal remains of these species can be found in large numbers in lacustrine sediments and over a wide north–south range in Europe. The total length of both headshield and postabdomen for A. affinis and A. quadrangularis and carapace length for C. cf. sphaericus were measured to observe their response to changes in latitude and temperature. A different response to ambient temperature in the growth of body parts was observed. The size of the headshields of both Alona species and of the carapace of Chydorus was significantly larger in colder regions as opposed to warm ones. It turned out that the postabdomen was not a good predictor of ambient temperature. While the sizes of all remains increased with latitude, the sizes of the Alona remains was smaller in the mountain lakes of the Southern Carpathians than in other cold lakes, in this case in Finland, a fact indicative of the importance of other factors on size distribution. This study demonstrates that a morphological response to climate is present in littoral cladocerans, and, therefore, changes in the length of headshield and carapace may be used as a proxy for climate changes in paleolimnological records.

Appels met (kwee)peren vergelijken

Comparing apples, quinces and pears. While establishing the identification possibilities of subfossil plant tissues derived from cesspits, the following question arose: is variation within species a limiting factor for establishing diagnostic characteristics? In order to answer this question core fragments of modern fruits of Apples, Quinces and Pears were examined. These fragments are frequently encountered during archaeobotanical analyses of cesspits. However, they are rarely identified to a species level, due to a lack of criteria for identification. This study also aims to provide criteria for identification in addition to visual reference material. A comparison of modern and subfossil remains revealed that the characteristics of Apple and Quince show similarities, which complicates the identification possibilities of these two species. However, it is possible to distinguish between the core fragments of Apple and Pear.

Widespread male sex bias in mammal fossil and museum collections

A recent study of mammoth subfossil remains has demonstrated the potential of using relatively low-coverage high-throughput DNA sequencing to genetically sex specimens, revealing a strong male-biased sex ratio [P. Pečnerová et al., Curr. Biol. 27, 3505–3510.e3 (2017)]. Similar patterns were predicted for steppe bison, based on their analogous female herd-based structure. We genetically sexed subfossil remains of 186 Holarctic bison (Bison spp.), and also 91 brown bears (Ursus arctos), which are not female herd-based, and found that ∼75% of both groups were male, very close to the ratio observed in mammoths (72%). This large deviation from a 1:1 ratio was unexpected, but we found no evidence for sex differences with respect to DNA preservation, sample age, material type, or overall spatial distribution. We further examined ratios of male and female specimens from 4 large museum mammal collections and found a strong male bias, observable in almost all mammalian orders. We suggest that, in mammals at least, 1) wider male geographic ranges can lead to considerably increased chances of detection in fossil studies, and 2) sexual dimorphic behavior or appearance can facilitate a considerable sex bias in fossil and modern collections, on a previously unacknowledged scale. This finding has major implications for a wide range of studies of fossil and museum material.

Pigeons, sandgrouse, cuckoos, nightjars, rollers, bee-eaters, kingfishers and swifts in the European fossil avifauna and their osteological characteristics

In the article, the author describes the presence of fossil records of the pigeons (Ord. Columbiformes, Fam. Columbidae), sandgrouse (Ord. Pteroclidiformes, Fam. Pteroclididae), cuckoos (Ord. Cuculiformes, Fam. Cuculidae), nightjars (Ord. Caprimulgiformes, Fam. Caprimulgidae), rollers (Ord. Coraciiformes, Fam. Coraciidae), bee-eaters (Ord. Coraciiformes, Fam. Meropidae), (Ord. Coraciiformes, Fam. Upupidae), kingfishers (Ord. Coraciiformes, Fam. Alcedinidae) and swifts (Ord. Apodiformes, Fam. Apodidae) in Europe, particularly the Carpathian Basin, during the Tertiary and Quaternary, as well as their osteological characteristics. These orders generally contain a small number of species in Europe, most of them consisting of thermophilic, migratory species. Their fossil and subfossil remains provide precious information about the climatic conditions of their respective areas of origin. The text is supplemented by 15 figures and 2 tables.

Osteological criteria for the specific identification of Monitor lizards (Varanus Merrem, 1820) remains in subfossil deposits of Sundaland and continental Southeast Asia

The identification at species level of subfossil remains of lizards from tropical regions currently suffers from strong limitation linked to the lack of comprehensive work conducted on the osteology of modern taxa. The aim of this study is to provide osteological criteria allowing for the specific identification of the subfossil remains of Sundaland and continental Southeast Asian monitor lizards (Varanus sp.), which are often well-represented in the deposits of this geographic area. To do so we performed an osteological study of the four species occurring in this region (V. bengalensis sensu lato, V. salvator, V. dumerilii, and V. rudicollis) using a large set of 88 skeletons of modern specimens. The observation of the full set of specimens allows us to define 41 osteological criteria distributed on 20 different anatomical parts which enable the specific identification of isolated bones of the studied species. The results highlight the importance of taking account of the morphological intraspecific variability by the use of large samples of specimens to avoid identification errors. They also show that the distinction of closely related taxa remains complex even when detailed morphological analyses are performed.

Littoral chironomids of a large Alpine lake: spatial variation and variables supporting diversity

Chironomidae are a major group of littoral secondary producers whose spatial changes in assemblage structures are shaped by diverse variables. Using their subfossil remains, we aimed at disentangling the relative impact of environmental, topographic, littoral occupation and hydrodynamic variables on the littoral assemblages as well as identifying taxa and sites of primary importance for the β-diversity in a large lake (Lake Bourget). A redundancy analysis coupled with a variance partitioning indicated that 22 % of the assemblage variability was explained by slope, carbonate concentration and littoral occupation. A non-negligible fraction of non-separable variance among these variables likely highlights the topographic constraint on anthropogenic development and environmental conditions. Taxonomic turnover overwhelmingly (93.2 %) dominated the assemblage changes indicating site-specific taxonomic composition. The taxa contribution to β-diversity was positively correlated with their mean abundances. The local abundances were either positively or negatively correlated with local contribution of sites to β-diversity (LCBD) providing evidence for different contributions of taxa to β-diversity. A couple of taxa (i.e.Cricotopusspp.,Microtendipessp. andCladotanytarsussp.) and sites (i.e.LB57, LB31, LB2) clearly supported the major variations of β-diversity and are therefore identified as being of primary importance regarding conservation programs. Both LCBD variations and taxa spatial autocorrelations suggest that chironomid assemblages were the most variable at a spatial-scale ranging from 500 m to 1 km, characterizing the spatial successions of littoral contexts. These results illustrate the need for considering short spatial scales to reveal the extent of the benthic diversity in the littoral areas of large lakes.