Human inbreeding has decreased in time through the Holocene

The history of human inbreeding is controversial. In particular, how the development of sedentary and/or agricultural societies may have influenced overall inbreeding levels is unclear. Here we present an approach for reliable estimation of runs of homozygosity (ROH) in genomes with ≥3x mean sequence coverage across >1 million SNPs, and apply this to 411 ancient Eurasian genomes from the last 15,000 years. We show that the frequency of inbreeding, as measured by ROH, has decreased over time. The strongest effect is associated with the Neolithic transition, but the trend has since continued, indicating a population size effect on inbreeding prevalence. We further show that most inbreeding in our historical sample can be attributed to small population size instead of consanguinity. We observed singular cases of high consanguinity only among members of farming societies

A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition

Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked innovations in symbolism, technology, and foodways. We present thirteen ancient genomes (c.8500-7500 calBCE) from Pre-Pottery Neolithic Çayönü in the Tigris basin together with bioarchaeological and material culture data. Our findings reveal that Çayönü was a genetically diverse population, carrying a mixed ancestry from western and eastern Fertile Crescent, and that the community received immigrants. Our results further suggest that the community was organised along biological family lines. We document bodily interventions such as head-shaping and cauterization among the individuals examined, reflecting Çayönü's cultural ingenuity. Finally, we identify Upper Mesopotamia as the likely source of eastern gene flow into Neolithic Anatolia, in line with material culture evidence. We hypothesise that Upper Mesopotamia's cultural dynamism during the Neolithic Transition was the product not only of its fertile lands but also of its interregional demographic connections

Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean

We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of complex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 present-day published genomes, we found that genetic diversity within each region steadily increased through the Holocene. We further observed that the inferred sources of gene flow shifted in time. In the first half of the Holocene, Southwest Asian and the East Mediterranean populations homogenized among themselves. Starting with the Bronze Age, however, regional populations diverged from each other, most likely driven by gene flow from external sources, which we term “the expanding mobility model.” Interestingly, this increase in inter-regional divergence can be captured by outgroup-f$_3$-based genetic distances, but not by the commonly used F$_{ST}$ statistic, due to the sensitivity of F$_{ST}$, but not outgroup-f$_3$, to within-population diversity. Finally, we report a temporal trend of increasing male bias in admixture events through the Holocene

Syntopic Occurrence in Turkey Supports Separate Species Status forMiniopterus schreibersii schreibersiiandM. schreibersii pallidus(Mammalia: Chiroptera)

Bilgin R, Gürün K, Maraci Ö, et al. Syntopic Occurrence in Turkey Supports Separate Species Status forMiniopterus schreibersii schreibersiiandM. schreibersii pallidus(Mammalia: Chiroptera). Acta Chiropterologica. 2013;14(2):279-289

Runs of homozygosity suggest a reduction in inbreeding through the Holocene

How the advent of agriculture and social complexity changed human inbreeding patterns is unclear. Ethnographic work suggests low levels of consanguinity in modern-day foragers compared to farmer communities. Meanwhile, the larger population sizes of farmer societies may have lowered the frequency of panmictic (i.e. drift-driven) inbreeding in these groups. Hence, the net impact of food production on autozygosity levels remains unknown. Here we show that runs of homozygosity (ROH) >1 Mb can be reliably estimated in genomes with ≥3x mean coverage per SNP. We thus calculate the ROH-based inbreeding coefficient estimate, or FROH, in 411 published ancient Eurasian genomes from the last 15,000 years. We find that FROH has significantly decreased over time, in both West and Central Eurasia. The most dramatic reduction appears associated with the Neolithic Transition. Our results hence suggest that population growth caused by food production, along withincreased rates of human mobility, reduced the frequency of panmictic inbreeding and led to a reduction in overall autozygosity. We find that cases of high consanguinity are rare in our sample and are restricted to individuals from farmer communities. Finally, we note that the high consanguinity levels observed in presentday Central Eurasia are not observed in ancient genomes, and this may therefore be a recent phenomenon

Circum-Mediterranean phylogeography of a bat coupled with past environmental niche modeling: A new paradigm for the recolonization of Europe?

Bilgin R, Gürün K, Rebelo H, et al. Circum-Mediterranean phylogeography of a bat coupled with past environmental niche modeling: A new paradigm for the recolonization of Europe? Molecular Phylogenetics and Evolution. 2016;99:323-336

Datzman_Layout 1

In contrast to the Eastern Palaearctic region a high degree of cryptic diversity was discovered among temperate bats of the Western Palaearctic region in the last ten years. Climatic oscillations caused severe changes in the distribution of species throughout the Palaearctic region during the Pleistocene. Exploring multiple taxa can help to understand general evolutionary differentiation processes. In the present study genetic variation within and among 94 Mongolian vespertilionid bats of six genera (Hypsugo, Eptesicus, Vespertilio, Myotis, Plecotus, and Nyctalus) was screened by sequencing a 798 bp fragment of the mitochondrial ND1 gene and then subsequently compared with those of Western Palaearctic taxa. This allowed first insights in the differentiation among a wide range of bats across the Palaearctic region. A total of 16 distinct mitochondrial lineages were found in Mongolia. Thirteen lineages differed by at least five percent sequence divergence from Western Palaearctic species. Only three lineages (Eptesicus nilssonii, Vespertilio murinus, and Nyctalus noctula) showed lower divergence values. Our data demonstrate a substantial differentiation between most Western and Eastern Palaearctic vespertilionid bats. Estimations of divergence times showed that most divergence appeared prior to the Pleistocene, but current distributions of bats were most likely shaped by the usage of multiple refugia during glaciations. Department of Mammalogy and Ornithology, Natural History Museum of Geneva, Geneva, We report the first records of Nyctalus plancyi from the Philippines, on the basis of three specimens taken in high-elevation mossy forest in the Central Cordillera of northern Luzon. We also report three new specimens of Falsistrellus petersi in the same areas, previously a poorly known species within the Philippines, and provide the first genetic data on the phylogenetic position of the genus. Analysis of sequence data from the mitochondrial gene cytochrome b shows ca. 4% divergence of the Philippine N. plancyi from a sample from China. Combined sequence data from cytochrome b and the nuclear gene RAG2 confirm that N. plancyi is related to Pipistrellus. They further show that F. petersi is related to Hypsugo and Vespertilio, and Philetor brachypterus is related to Tylonycteris, with all of these taxa being members of the Vespertilionini, not the Pipistrellini. Nyctalus plancyi is the first mammal species documented to have colonized the main, oceanic body of the Philippines from the north (i.e., Taiwan or mainland China), rather than from the south (Borneo, Sulawesi, or New Guinea). The taxonomic position of Bobrinski's serotine (Eptesicus bobrinskoi) is still unclear. In the present study the relationships between E. bobrinskoi and other small Palaearctic serotines were examined based on morphometric and molecular evidence. Both mitochondrial (cytochrome b) and nuclear (THY) sequence data indicate that E. bobrinskoi is closely related to Gobi serotine (E. gobiensis). The difference between these two forms is significantly lower than between either of them and any other Palaearctic serotine. The results of morphometric analysis suggest that morphological differentiation between E. gobiensis and E. bobrinskoi is to a large extent accounted for by size difference. It is concluded that the species status of Bobrinski's serotine is doubtful and this bat should be treated as a subspecies of E. gobiensis. Metropolitana -Iztapalapa, Av. San Rafael Atlixco N° 186, Col. Vicentina, C.P. 09340, Iztapalapa, México D.F. 3 Estación Biológica de Doñana, C.S.I.C., A.P. 1056, 41080 Sevilla, España 4 Corresponding author: E-mail: [email protected] Due to its morphological conservatism, the American funnel-eared bats of the genus Natalus have had a complex taxonomic history. In Mexico only one species, N. stramineus, has traditionally been recognized. But recently a new endemic species, N. lanatus, was described in the region as a sympatric sibling species of N. stramineus. Natalus stramineus, with a geographic distribution extending from Mexico to Panama, was subsequently reassigned to N. mexicanus. In this study, we analyzed morphological and molecular characters to determine if two distinct species of funnel-eared bats (N. lanatus and N. mexicanus) occur in Mexico. We found that the proposed diagnostic morphological characters that separate the two taxa are not consistent and rarely differentiate between the two forms. Likewise, phylogenetic analyses do not support the separation of Natalus into two species in Mexico, but there is clearly geographic structure when all Mexican haplotypes are combined. The genetic distance between the haplotypes that could be ascribed to N. lanatus and N. mexicanus was typically within the range of conspecifics and not distinct species. To summarize, the results of both morphological and molecular analyses point to the presence of a single species of Natalus in Mexico. The original description for Anoura fistulata (long-lipped bat) was mostly qualitative in nature. Here we make a quantitative reassessment of morphological variation in skull shape for this and other Ecuadorian species. Our goal is to provide a perspective into morphospace for understanding the boundaries and extent of variation within and among species of Anoura occurring in Ecuador. Our results show that, besides its singular differences in soft-tissue anatomy, the distribution of samples in morphospace for A. fistulata suggests this species occupies an intermediate space between A. geoffroyi and A. caudifer. Anoura geoffroyi and A. caudifer share opposite regions of morphospace, where size is the largest factor contributing to variation, and along the shape vector both species are distinguished mostly by a contraction of the maxilla and a contraction of the braincase, respectively. Although size is the main factor determining boundaries among species, for A. cultrata shape seems to be more relevant, as its geometric configuration of the skull is remarkably different. The other species are similar in shape when size is factored out. An unusual group of specimens may require further study as they may represent an unknown species, as these occupy unexpected areas of morphospace. A discussion of why we do not think there is evidence to assign this unusual group to any of the small species of Anoura (i.e. A. caudifer, A. aequatoris, and A. luismanueli) is also included. Populations of A. geoffroyi from the western and eastern slopes of the Andes show statistically supported differences in most of the measured morphological traits, however this is not true for A. caudifer. The effect of western and eastern habitats on the geometric configuration of the skull is different and inverted between both species. This results in a statistical interaction between the two slopes of the Andes and the two species. Eastern populations of A. geoffroyi and A. caudifer are morphologically closer than western populations in both species. Anoura geoffroyi possesses a larger altitudinal range and a larger body size, a positive correlation that may concur with the hypothesis of body size serving as a buffer to extreme or highly variable environments. The frequency distribution of character states in morphospace and their differentiation across the various species of Anoura is discussed in the context of diet and habitat. A diverse syntopic bat community was studied in Central Europe. The study was primarily aimed at forest bats utilizing a foliagegleaning foraging strategy (Myotis nattereri, M. bechsteinii and Plecotus auritus). The results indicated the foliage-gleaning foraging strategy and the effective resource partitioning. Once a certain diet item comprises an important food resource for one bat species, it is usually exploited much less by the other two bat species, and despite important seasonal dietary changes this pattern lasts throughout the entire season. Dietary composition varies more among the entire guild of forest foliage-gleaning bats than it does between these species and their morphological siblings or evolutionarily related species (e.g., Plecotus auritus vs. P. austriacus or Barbastella barbastellus, Myotis nattereri vs. M. emarginatus). The results are not fully consistent with the predictions of sensory ecology, which presume that bats with longer ears feed more frequently on prey that generates sound. The results do not support the hypothesis that rare bats exploit a narrower range of prey. The relatively rare M. bechsteinii has a wider trophic niche, whereas the more common P. auritus exploits a narrower range of prey. Comparison of dietary composition and morphological and echolocation parameters indicates that larger species feed on harder prey, species with longer ears are moth-eating specialists and species with a higher call intensity exploit small dipterans, probably in uncluttered habitats. Most European bat species are insectivorous and share foraging areas to some extent. Where similar species rely on similar resources in the same foraging habitat, they are likely to interact. This study addresses the trophic niche of the Northern European trawling bat species Myotis dasycneme (Boie, 1825) and Myotis daubentonii (Kuhl, 1817), occurring in the same habitat, and possible interactions or differences within their dietary behaviour. Dietary data of both species were analysed to draw conclusions on their ecology, possible dietary overlap, hints for coexistence mechanisms and community structure. In this study, M. dasycneme and M. daubentonii fed mainly on Chironomidae (M. dasycneme: 44.4%; M. daubentonii: 32.8%) and Trichoptera (M. dasycneme: 20.4%; M. daubentonii: 22.2%), showing a high trophic niche overlap and similar niche breadth. Nevertheless, there were differences in the diet of the two species concerning the predation of chironomids. Differences also occur regarding the prey types, referring to the terrestrial or aquatic life-cycle of prey groups. This could be evidence for different foraging habitats and a spatial segregation of both species. High resource abundance is also likely to allow the coexistence of both species within the same hunting habitat. Seed dispersal is a key process for plant colonization and for the establishment of many plant populations in tropical environments. A large proportion of all tropical woody plants with fruits and seeds depend on frugivorous vertebrates for their dispersal, and frugivorous bats are essential for the dispersal of seeds from many tropical plants. Many of these plants are important for vegetative regeneration after disturbances. Our main goal was to document the process of seed dispersal through feces-seed analysis by the bat community among semi-deciduous, evergreen, and secondary forests in the 'Huasteca' region of San Luis Potosí, Mexico. We hypothesized that bats would disperse seeds among all three forest types, and thus predicted that we would find seeds from both early and late successional stages in bat feces in all three forest types. In each of three replicate sites representative of each of these forest types, we trapped bats with mist-nets and collected their feces with seeds. A total of 558 individuals from eight frugivorous bat species were captured. The most abundant species were Sturnira ludovici, Glossophaga soricina and Artibeus jamaicensis. We documented seeds in bat feces from 16 plant species belonging to four families: Moraceae, Piperaceae, Solanaceae, and Myrtaceae; 43% were pioneer species, and thus important for the initial stages of regeneration, and 37% were species of late successional stages. Seeds in bat feces were found in similar proportions in all forest types, thus contributing to the regeneration of highly deforested habitats in the Huasteca region. To maintain the entire mutualistic network between bats and plant species, diverse bat communities are important. Dietary differentiation can be a key mechanism for the coexistence of syntopic species with similar niches. On the Caribbean island of Puerto Rico, three species of bat from the family Mormoopidae -the Antillean ghost-faced bat (Mormoops blainvillei), sooty mustached bat (Pteronotus quadridens), and Parnell's mustached bat (Pteronotus parnellii portoricensis) -are aerial insectivores that roost in the same caves. To investigate the possibility of dietary differentiation, we estimated the percent volume and percent frequency of occurrence of the orders of arthropods consumed by these three species of bat, using standard fecal analysis. We also compared dietary diversity among species, as well as the amount of dietary overlap, with respect to season and habitat. Lastly, this study used canonical correspondence analysis (CCA), a method of ordination, to assess the effects of species, sex, age, reproductive condition, season, and habitat on intraspecific differences in the diet of the Puerto Rican Mormoopidae. Eight orders of arthropods were found in the diet of these mormoopids, with Lepidoptera, Hymenoptera, and Coleoptera being major staples. The CCA revealed differences in diet among the three species, suggesting that dietary differentiation is at least one mechanism for coexistence. In addition, the variables habitat and season correlated significantly with the diet of M. blainvillei and P. quadridens, whereas habitat and sex correlated with the diet of P. p. portoricensis. Thus, our study shows dietary differences among the three species of Mormoopidae living in the same caves on Puerto Rico, as well as intraspecific differences within the diet of each species. Populations of Pipistrellus nathusii (Nathusius's bat), an insectivorous aerial-hawking species that breeds in north-eastern Europe, perform long-distance migrations between breeding sites and hibernation areas in central and southern Europe. The feeding strategy of migrating P. nathusii was investigated in Latvia on the east coast of the Baltic Sea, exploring evidence for and against two non-mutually exclusive predictions that i) the bats feed shortly after dusk at highest aerial insect activity and continue to migrate thereafter or ii) apply a 'fly-and-forage' strategy and frequently interrupt their migration flight to feed. Echolocation calls and feeding buzzes of P. nathusii were recorded throughout the night from August until September on a known migration flyway over coastal dunes and at potential foraging sites in adjacent woodlands, over meadows and wetlands. The results indicate that P. nathusii applies a fly-and-forage strategy along the Baltic coast. However, a threshold in aerial insect availability may exist, below which no foraging occurs and migration continues. Most flying fox species (genus Pteropus) exhibit strong coloniality. They are highly mobile animals and commonly forage over vast areas. Only a small number of species are solitary, and their foraging and roosting patterns are not well understood. Here, we examined ranging patterns and habitat use of Orii's flying fox, Pteropus dasymallus inopinatus, a solitary fruit bat, using radiotracking from April 2002 to January 2006 on Okinawa-jima Island, Ryukyu Archipelago, Japan. The daily home range size for this species was very small (mean 52.5 ha) compared to other Pteropus species, although home range size was highly variable among individuals and seasons. The distance between a day roost and feeding trees was 621 m on average, with a maximum of 6,875 m. Day roost site shifted frequently (every 1.6 ± 0.8 days) to a nearby site in the current foraging area. The distance between consecutive day roost sites was 792 m on average, with a maximum of 6,000 m. These bats favored forest habitats for roosting sites, whereas they often used residential areas as feeding sites. Our results suggest that they regularly shifted the location of their personal activity range, a small home range with roost switching, probably to track changes in food availability and to avoid local competition for food. The solitary roosting system of this species links to its flexible foraging system, which likely provides an advantage for using limited food resources on a small island, even when food is patchily distributed in urbanized habitats. The effects of detector height and season on bat activity have not been investigated in the UK and are poorly understood globally, yet are crucial to designing effective acoustic activity surveys. The aim of this study was to test predictions of species foraging preferences for the canopy or understorey and to determine whether this pattern shows seasonal variation. Bat activity was recorded using automated detectors in the canopy and understorey of an ancient broadleaved woodland in south-west England in spring and summer for a total of 40 nights. Activity levels were then compared between each of the two detector heights and two seasons. The canopy detector recorded significantly more bat activity overall and recorded significantly higher activity of Nyctalus, Pipistrellus pipistrellus and P. pygmaeus compared to the understorey detector. Nyctalus were more frequent in summer compared to spring. Pipistrellus pipistrellus consistently preferred the canopy, whilst P. pygmaeus showed this preference in summer only. Myotis were more frequent in spring compared to summer, favouring the understorey in spring but displaying a marginal preference for the canopy in summer. This suggests that it is advisable to record at multiple heights at different stages of the active season to assess bat activity in woodland. These effects should be tested in other woodland sites in order to determine the consequences of groundbased recording during a limited survey period. The vocalizations of the Malagasy endemic fruit bat, Eidolon dupreanum (family Pteropodidae) were previously not documented. Individuals of this species, which make day roost sites in rock crevices or the dark zones within caves, were recorded while exiting a cave in the Parc National d'Ankarana. Individuals leaving a roost at dusk were recorded 200 m and 35 m inside the cave, as well as two sites outside the cave. Visible light in the cave dropped to 0 lux about 50 m from the entrance. While exiting, individuals flew within 50-100 cm of the ceiling, often settling and perching every 5-10 m along their flight patch and displacing in a leapfrog manner towards the cave entrance. Three distinct call types were identified: social calls 1, social calls 2 and echo clicks. Bats produce the echo clicks while flying towards the entrance, while the other two calls were emitted at roost sites and near the cave entrance. Although the results are preliminary, we suggest that the social calls 1 and 2 were employed for social communication, whilst echo clicks may have been used in a sensory context, potentially as incipient echolocation to navigate in the dark cave. Since the behavior of hibernating bats is usually affected by varying environmental conditions we measured changes in the ambient temperature (T a ) and water vapor pressure (WVP) and their variability in the selected areas and analyzed the relationship between clustering behavior of hibernating bats and abiotic conditions. In both winters, the number of solitarily roosting individuals of M. myotis decreased from autumn to spring while the highest number of bats hibernating in clusters was recorded in the middle of winter. The number of clusters did not change significantly over the winter, but the number of individuals within a particular cluster increased from November (median = 5, inter-quartile range, IQR = 5-8) to March (median = 20, IQR = 14-35.5). The changes of the clusters' size were best explained by a mixed model with WVP and the variability in WVP over the 20 days prior to the bat survey as explanatory variables. As WVP and the variability in WVP decreased, the number of individuals in a cluster increased. Also, T a affected the size of clusters. However, neither of the models supported the hypothesis of the effect of variability of T a on clustering of M. myotis. We propose that huddling enables bats to reduce evaporative water loss during the middle and at the end of the hibernation and reduces costs of spring arousals, perhaps by synchronizing them between clustered individuals and thus allowing the use of passive re-warming. The impact of climate change on different species has been analyzed many times in various geographical areas. However, some areas still have a large knowledge gap while harbouring significant levels of biodiversity. The main aim of this study was to determine how climate change will affect 16 different bat species in the Eastern Mediterranean Region. Using presence only modelling techniques and relevant bioclimatic data forecasts according to two different climate change scenarios (A2A and B2A) of the Intergovernmental Panel on Climate Change (IPCC), the potential geographic distribution of bat species in the eastern Mediterranean region for the current period and the years 2020, 2050 and 2080 were modelled. The results suggest that climate change can affect bats negatively throughout the 21st century in the studied area on two fronts: i) species richness will deteriorate, and ii) the total area occupied by bats will decline. These impacts are likely to be more severely observed in Turkey's coastal areas, northwest Turkey, Red Sea coasts, Israel, and the west of Syria and Jordan. Using only bioclimatic variables as factors, and thus not using any land cover (or habitat) data, was the main limitation of the study. Hence the models and results of the study present 'best case' scenarios. Our study aims to determine how different climatic varia