Because many bird species are monomorphic or only sexually dimorphic in adult stages, it is difficult to determine their sexes, which may cause significant problems in population and conservation ...studies. DNA-based sexing relies on the chromodomain helicase DNA binding (CHD) gene located on the W chromosome and its homolog on the Z chromosome, giving distinct banding patterns on agarose gel as a result of length differences in intronic regions within this gene. We used 3 specific primer sets, CHD1F/CHD1R, 2550F/2718R, and P2/P8, for sex determination of 230 samples from 77 avian species. We report here the records for 70 of those species analyzed using the CHD1F/CHD1R primer set, and 49 species using 2550F/2718R, and 46 species using P2/P8. CHD1F/CHD1R PCR products on agarose gel generally showed an apparent single band in males and 2 bands in females, but the products of 2550F/2718R (61%) and P2/P8 (42%) showed distinct banding patterns for separate bird orders. However, when PCR products of these last 2 primer pairs labeled with fluorescent dye were run in a capillary gel and detected using a DNA analyzer, P2/P8 gave 2 distinguishable peaks in females, whereas 2550F/2718R results remained the same. DNA sexing with any of those 3 primer sets can be used for all sexually monomorphic avian taxa although the primer sets should be compared before choosing the most efficient one for molecular sexing of the studied species.
Our aims were to assess the phylogeographic patterns of genetic diversity in eastern Mediterranean water frogs and to estimate divergence times using different geological scenarios. We relate ...divergence times to past geological events and discuss the relevance of our data for the systematics of eastern Mediterranean water frogs. The eastern Mediterranean region. Genetic diversity and divergence were calculated using sequences of two protein-coding mitochondrial (mt) genes: ND2 (1038 bp, 119 sequences) and ND3 (340 bp, 612 sequences). Divergence times were estimated in a Bayesian framework under four geological scenarios representing alternative possible geological histories for the eastern Mediterranean. We then compared the different scenarios using Bayes factors and additional geological data. The extensive genetic diversity in mtDNA divides eastern Mediterranean water frogs into six main haplogroups (MHGs). Three MHGs were identified on the Anatolian mainland; the most widespread MHG with the highest diversity is distributed from western Anatolia to the northern shore of the Caspian Sea, and includes the type locality of Pelophylax ridibundus. The other two Anatolian MHGs are restricted to south-eastern Turkey, occupying localities west and east of the Amanos mountain range. One of the remaining three MHGs is restricted to Cyprus; the second, to the Levant; and the third was found in the distribution area of European lake frogs (P. ridibundus group), including the Balkans. Based on geological evidence and estimates of genetic divergence we hypothesize that the water frogs of Cyprus have been isolated from the Anatolian mainland populations since the end of the Messinian salinity crisis (MSC), that is, since c. 5.5-5.3 Ma, while our divergence time estimates indicate that the isolation of Crete from the mainland populations (Peloponnese, Anatolia) probably pre-dates the MSC. The observed rates of divergence imply a time window of c. 1.6-1.1 million years for diversification of the largest Anatolian MHG; divergence between the two other Anatolian MHGs may have begun about 3.0 Ma, apparently as a result of the uplift of the Amanos Mountains. Our mtDNA data suggest that the Anatolian water frogs and frogs from Cyprus represent several undescribed species.
We present palaeogenomes of three morphologically unidentified Anatolian equids dating to the first millennium BCE, sequenced to a coverage of 0.6–6.4×. Mitochondrial DNA haplotypes of the Anatolian ...individuals clustered with those of Equus hydruntinus (or Equus hemionus hydruntinus), the extinct European wild ass, secular name ‘hydruntine’. Further, the Anatolian wild ass whole genome profiles fell outside the genomic diversity of other extant and past Asiatic wild ass (E. hemionus) lineages. These observations suggest that the three Anatolian wild asses represent hydruntines, making them the latest recorded survivors of this lineage, about a millennium later than the latest observations in the zooarchaeological record. Our mitogenomic and genomic analyses indicate that E. h. hydruntinus was a clade belonging to ancient and present‐day E. hemionus lineages that radiated possibly between 0.6 and 0.8 Mya. We also find evidence consistent with recent gene flow between hydruntines and Middle Eastern wild asses. Analyses of genome‐wide heterozygosity and runs of homozygosity suggest that the Anatolian wild ass population may have lost genetic diversity by the mid‐first millennium BCE, a possible sign of its eventual demise.
The social organization of the first fully sedentary societies that emerged during the Neolithic period in Southwest Asia remains enigmatic,1 mainly because material culture studies provide limited ...insight into this issue. However, because Neolithic Anatolian communities often buried their dead beneath domestic buildings,2 household composition and social structure can be studied through these human remains. Here, we describe genetic relatedness among co-burials associated with domestic buildings in Neolithic Anatolia using 59 ancient genomes, including 22 new genomes from Aşıklı Höyük and Çatalhöyük. We infer pedigree relationships by simultaneously analyzing multiple types of information, including autosomal and X chromosome kinship coefficients, maternal markers, and radiocarbon dating. In two early Neolithic villages dating to the 9th and 8th millennia BCE, Aşıklı Höyük and Boncuklu, we discover that siblings and parent-offspring pairings were frequent within domestic structures, which provides the first direct indication of close genetic relationships among co-burials. In contrast, in the 7th millennium BCE sites of Çatalhöyük and Barcın, where we study subadults interred within and around houses, we find close genetic relatives to be rare. Hence, genetic relatedness may not have played a major role in the choice of burial location at these latter two sites, at least for subadults. This supports the hypothesis that in Çatalhöyük,3–5 and possibly in some other Neolithic communities, domestic structures may have served as burial location for social units incorporating biologically unrelated individuals. Our results underscore the diversity of kin structures in Neolithic communities during this important phase of sociocultural development.
•Genetic kinship estimated from co-buried individuals’ genomes in Neolithic Anatolia•Close relatives are common among co-burials in Aşıklı and Boncuklu•Many unrelated infants found buried in the same building in Çatalhöyük and Barcın•Neolithic societies in Southwest Asia may have held diverse concepts of kinship
Yaka et al. use ancient genomes from Neolithic Anatolia and present evidence for diverse concepts of social kinship in Neolithic societies. In some communities, like Çatalhöyük, many genetically unrelated infants were buried together inside the same buildings, whereas in other sites, people buried together were frequently close biological kin.
•Altitudinal gradient and human activities shape bird communities of Inner Anatolia.•Avian diversity increased with reduced grazing and proximity to rural settlements.•Steppe-dependent bird diversity ...was highest in cropland abandoned 20–50 years ago.
We present here the first systematic study on drivers of bird community composition and diversity in Anatolian steppes (Turkey), an environment important for populations of threatened grassland birds yet underrepresented in conservation networks. We focused on one million hectares of mountainous land with a long and varied land use history, and collected quantitative data on breeding birds as well as environmental, vegetation, landscape and land use parameters at 32 sites. Data were analyzed by canonical correspondence analysis (CCA) and hierarchical partitioning to understand avian community structure and reveal major drivers of observed patterns. Bird communities in high-altitude steppes of inner Turkey showed patterns in species richness and community composition that were best explained by an altitudinal gradient and by human activities. Steppe birds occurred most often in cropland abandoned 20–50 years ago with good coverage of erect leafy plants while overall avian diversity tended to increase with reduced grazing pressure and with nearby presence of rural settlements. CCA results revealed a contrast between highly heterogeneous anthropogenic environments in warmer and drier land with woody elements, and treeless steppes at higher elevations that were, apart from transhumant grazing, little influenced by human activities. The former sites were characterized by the occurrence of several grassland birds along with a variety of generalist species, some of which required the presence of trees, while the latter sites were less diverse but usually with a higher proportion of steppe-dependent birds in their composition. To conserve steppes for birds, we recommend as key actions to maintain the current landscape mosaic, sustain low to moderate grazing levels and use our findings in developing a network of protected areas.
Abstract
Communication often happens in noisy environments where interference from the ambient noise and other signalers may reduce the effectiveness of signals which may lead to more conflict ...between interacting individuals. Signalers may also evolve behaviors to interfere with signals of opponents, for example, by temporally overlapping them with their own, such as the song overlapping behavior that is seen in some songbirds during aggressive interactions. Song overlapping has been proposed to be a signal of aggressive intent, but few studies directly examined the association between song overlapping and aggressive behaviors of the sender. In the present paper, we examined whether song overlapping and ambient noise are associated positively with aggressive behaviors. We carried out simulated territorial intrusions in a population of great tits (Parus major) living in an urban–rural gradient to assess signaling and aggressive behaviors. Song overlapping was associated negatively with aggressive behaviors males displayed against a simulated intruder. This result is inconsistent with the hypothesis that song overlapping is an aggressive signal in this species. Ambient noise levels were associated positively with aggressive behaviors but did not correlate with song rate, song duration, or song overlapping. Great tits in noisy urban habitats may display higher levels of aggressive behaviors due to either interference of noise in aggressive communication or another indirect effect of noise.
Overlapping a rival’s song with one’s own is associated with lower aggression, while ambient noise is associated with higher aggression in male great tits. Male great tits holding territories in areas that vary from noisy urban habitats to quieter forest habitats respond differently to intruders depending on the ambient noise levels. However, they do not appear to signal their aggressive intent by starting to sing while their opponent is still singing.
The Anatolian Biogeographical Region is unique in the Palearctic realm, with high plant and butterfly species richness and populations of globally threatened birds, mammals and herptiles (amphibians ...and reptiles). It is a place of diverse land-use practices, dating back to the earliest farming practices in the world. Among 10,930 species of vascular plants, birds, butterflies, mammals and herptiles distributed in Turkey, we identified 1130 living predominantly in steppic environments and being classified either as threatened, near-threatened or data deficient at the national level, if not globally. A total of 28 effective protected areas were present in the region, covering 1.5 % of the 391,597 km
2
land area. Only 16.2 % of the threatened and near-threatened species (
n
= 809) were distributed within the protected area network, ranging from 94.1 % for birds to as low as 12.9 % for vascular plants. The total area of steppe and steppe forest vegetation has been reduced by at least 44 % of its former extent due to diverse habitat destructive activities. The most significant threats arise from unsustainable agricultural activities including overgrazing, conversion to croplands and afforestation. To maintain steppe diversity, we propose a “to-do list”, including mainstreaming biodiversity, effective implementation of Turkey’s Rangeland Act, conducting effective environmental impact assessments, establishing an effective site network for steppe biodiversity conservation and filling gaps in scientific knowledge.
Frogs have been harvested from the wild for the last 40 years in Turkey. We analysed the population dynamics of Anatolian water frogs (Pelophylax spp.) in the Seyhan and Ceyhan Deltas during ...2013–2015. We marked a total of 13,811 individuals during 3 years, estimated population sizes, simulated the dynamics of a harvested population over 50 years, and collated frog harvest and export statistics from the region and for Turkey as a whole. Our capture estimates indicated a population reduction of c. 20% per year, and our population modelling showed that, if overharvesting continues at current rates, the harvested populations will decline rapidly. Simulations with a model of harvested population dynamics resulted in a risk of extinction of > 90% within 50 years, with extinction likely in c. 2032. Our interviews with harvesters revealed their economic dependence on the frog harvest. However, our results also showed that reducing harvest rates would not only ensure the viability of these frog populations but would also provide a source of income that is sustainable in the long term. Our study provides insights into the position of Turkey in the ‘extinction domino’ line, in which harvest pressure shifts among countries as frog populations are depleted and harvest bans are effected. We recommend that harvesting of wild frogs should be banned during the mating season, hunting and exporting of frogs < 30 g should be banned, and harvesters should be trained on species knowledge and awareness of regulations.
Sheep were among the first domesticated animals, but their demographic history is little understood. Here we analyzed nuclear polymorphism and mitochondrial data (mtDNA) from ancient central and west ...Anatolian sheep dating from Epipaleolithic to late Neolithic, comparatively with modern-day breeds and central Asian Neolithic/Bronze Age sheep (OBI). Analyzing ancient nuclear data, we found that Anatolian Neolithic sheep (ANS) are genetically closest to present-day European breeds relative to Asian breeds, a conclusion supported by mtDNA haplogroup frequencies. In contrast, OBI showed higher genetic affinity to present-day Asian breeds. These results suggest that the east-west genetic structure observed in present-day breeds had already emerged by 6000 BCE, hinting at multiple sheep domestication episodes or early wild introgression in southwest Asia. Furthermore, we found that ANS are genetically distinct from all modern breeds. Our results suggest that European and Anatolian domestic sheep gene pools have been strongly remolded since the Neolithic.
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