The valley of Cuatro Ciénegas, an aquatic oasis located in the Mexican Chihuahuan Desert, exhibits the highest level of endemism in North America and is a Mexican National Protected Area. However, little is known about the evolutionary distinctiveness of several vertebrate species present in the Cuatro Ciénegas valley. We conducted a phylogeographic study using mitochondrial haplotypes from the centrarchid fish Lepomis megalotis to determine if the populations found within the valley were evolutionarily distinct from populations outside the valley. We also examined if there was evidence of unique haplotypes of this sunfish within the valley. Genetic divergence of L. megalotis suggests populations within the valley are evolutionarily unique when compared to L. megalotis outside the valley. Significant mitochondrial sequence divergence was also discovered between L. megalotis populations on either side of the Sierra de San Marcos that bisects the valley. Our results reinforce previous studies that suggest the organisms occupying aquatic habitats not only within Cuatro Ciénegas but also in each of the two lobes of the valley generally deserve independent consideration during management decisions.
The Out-of-Africa model holds that anatomically modern humans (AMH) evolved and dispersed from Africa into Asia, and later Europe. Palaeoanthropological evidence from the Near East assumes great importance, but AMH remains from the region are extremely scarce. ‘Egbert’, a now-lost AMH fossil from the key site of Ksar Akil (Lebanon) and ‘Ethelruda’, a recently re-discovered fragmentary maxilla from the same site, are two rare examples where human fossils are directly linked with early Upper Palaeolithic archaeological assemblages. Here we radiocarbon date the contexts from which Egbert and Ethelruda were recovered, as well as the levels above and below the findspots. In the absence of well-preserved organic materials, we primarily used marine shell beads, often regarded as indicative of behavioural modernity. Bayesian modelling allows for the construction of a chronostratigraphic framework for Ksar Akil, which supports several conclusions. The model-generated age estimates place Egbert between 40.8–39.2 ka cal BP (68.2% prob.) and Ethelruda between 42.4–41.7 ka cal BP (68.2% prob.). This indicates that Egbert is of an age comparable to that of the oldest directly-dated European AMH (Peştera cu Oase). Ethelruda is older, but on current estimates not older than the modern human teeth from Cavallo in Italy. The dating of the so-called “transitional” or Initial Upper Palaeolithic layers of the site may indicate that the passage from the Middle to Upper Palaeolithic at Ksar Akil, and possibly in the wider northern Levant, occurred later than previously estimated, casting some doubts on the assumed singular role of the region as a locus for human dispersals into Europe. Finally, tentative interpretations of the fossil's taxonomy, combined with the chronometric dating of Ethelruda's context, provides evidence that the transitional/IUP industries of Europe and the Levant, or at least some of them, may be the result of early modern human migration(s).
Based on specimens from the Lower Cretaceous Tlayua Formation of Mexico, we describe a new genus and species of Halecomorphi, Cipactlichthysscutatus gen. et sp. nov, which exhibits several diagnostic characters such as the dermal bones and the scales with ganoin and highly ornamented by numerous tubercles and ridges; parietal slightly longer than wide with approximately the same length as the frontal; jaws extending far, below the posterior orbital margin, reaching the posterior third of the postorbital plate; maxilla with a convexly rounded posterior margin; pectoral fin margins slightly convex; first ray of pectoral fin very long, reaching the posterior edge of the pelvic fin; about 37 preural vertebrae and 7 Ural centra; a series of hypertrophied scales just posterior to the cleithrum; arrangement of flank scales with two rows of deep scales; a series of dorsal and ventral scutes forming the dorsal and ventral midline, between the dorsal and anal fins and the caudal fin. A phylogenetic analysis including two outgroups and eleven neopterygians confirmed the monophyly of the Holostei as well as the monophyly of the Halecomorphi, although this last clade is weakly supported. Cipactlichthysscutatus was hypothesised as the sister-group of the (Ionoscopiformes + Amiiformes).
The fossil record of Peronosporomycetes (water moulds) is rather sparse, though their distinctive ornamentation means they are probably better reported than some true fungal groups. Here we describe a rare Palaeozoic occurrence of this group from a Guadalupian (Middle Permian) silicified peat deposit in the Bainmedart Coal Measures, Prince Charles Mountains, Antarctica. Specimens are numerous and comprise two morphologically distinct kinds of ornamented oogonia, of which some are attached to hyphae by a septum. Combresomyces caespitosus sp. nov. consists of spherical oogonia bearing densely spaced, long, hollow, slender, conical papillae with multiple sharply pointed, strongly divergent, apical branches that commonly form a pseudoreticulate pattern under optical microscopy. The oogonia are attached to a parental hypha by a short truncated stalk with a single septum. Combresomyces rarus sp. nov. consists of spherical oogonia bearing widely spaced, hollow, broad, conical papillae that terminate in a single bifurcation producing a pair of acutely divergent sharply pointed branches. The oogonium bears a short truncate extension where it attaches to the parental hypha. We propose that similarities in oogonium shape, size, spine morphology and hyphal attachment between the Permian forms from the Prince Charles Mountains and other reported Peronosporomycetes from Devonian to Triassic strata at widely separated localities elsewhere in the world delimit an extinct but once cosmopolitan Palaeozoic to early Mesozoic branch of the peronosporomycete clade. We name this order Combresomycetales and note that it played an important role in late Palaeozoic and early Mesozoic peatland ecosystems worldwide.
To understand the origin of Pantepui montane biotas, we studied the biogeography of toucanets in the genus Aulacorhynchus. These birds are ideal for analyzing historical relationships among Neotropical montane regions, given their geographic distribution from Mexico south to Bolivia, including northern Venezuela (Cordillera de la Costa), and the Pantepui. Analyses were based on molecular phylogenies using mitochondrial and nuclear DNA sequences. Topology tests were applied to compare alternative hypotheses that may explain the current distribution of Aulacorhynchus toucanets, in the context of previous hypotheses of the origin of Pantepui montane biotas. Biogeographic reconstructions in RASP and Lagrange were used to estimate the ancestral area of the genus, and an analysis in BEAST was used to estimate a time framework for its diversification. A sister relationship between the Pantepui and Andes+Cordillera de la Costa was significantly more likely than topologies indicating other hypothesis for the origin of Pantepui populations. The Andes was inferred as the ancestral area for Aulacorhynchus, and the group has diversified since the late Miocene. The biogeographic patterns found herein, in which the Andes are the source for biotas of other regions, are consistent with those found for flowerpiercers and tanagers, and do not support the hypothesis of the geologically old Pantepui as a source of Neotropical montain diversity. Based on the high potential for cryptic speciation and isolation of Pantepui populations, we consider that phylogenetic studies of additional taxa are important from a conservation perspective.
The origins of flora and fauna that are only found in Ireland and Iberia, but which are absent from intervening countries, is one of the enduring questions of biogeography. As Southern French, Iberian and Irish populations of the land snail Cepaea nemoralis sometimes have a similar shell character, we used mitochondrial phylogenies to begin to understand if there is a shared “Lusitanian” history. Although much of Europe contains snails with A and D lineages, by far the majority of Irish individuals have a lineage, C, that in mainland Europe was only found in a restricted region of the Eastern Pyrenees. A past extinction of lineage C in the rest of Europe cannot be ruled out, but as there is a more than 8000 year continuous record of Cepaea fossils in Ireland, the species has long been a food source in the Pyrenees, and the Garonne river that flanks the Pyrenees is an ancient human route to the Atlantic, then we suggest that the unusual distribution of the C lineage is most easily explained by the movements of Mesolithic humans. If other Irish species have a similarly cryptic Lusitanian element, then this raises the possibility of a more widespread and significant pattern.
The genus Calotriton includes two species of newts highly adapted to live in cold and fast-flowing mountain springs. The Pyrenean brook newt (Calotriton asper), restricted to the Pyrenean region, and the Montseny brook newt (Calotriton arnoldi), endemic to the Montseny massif and one of the most endangered amphibian species in Europe. In the present manuscript, we use an integrative approach including species distribution modeling (SDM), molecular analyses of mitochondrial and nuclear DNA sequence data and morphology to unravel the historical processes that have contributed to shaping the biogeography and genetic structure of the genus Calotriton, with special emphasis on the conservation of C. arnoldi. The results of the molecular analyses confirm that, despite having originated recently, being ecologically similar and geographically very close, there is no signal of hybridization between C. asper and C. arnoldi. SDM results suggest that tough environmental conditions on mountains tops during glacial periods, together with subsequent warmer periods could have prevented the contact between the two species. Within the critically endangered C. arnoldi, a high genetic structure is revealed despite its extremely small distribution range compared to C. asper. Haplotype networks, AMOVA and SAMOVA analyses suggest that two distinct groups of populations can be clearly differentiated with absence of gene flow. This is in concordance with morphological differentiation and correlates with its geographical distribution, as the two groups are situated on the eastern and western sides of a river valley that acts as a barrier. The genetic and morphological results are highly important for the ongoing conservation program of C. arnoldi and strongly justify the management of this species into at least two independent evolutionary significant units (eastern and western sectors) to guarantee the long-term population viability.
The only known albino gorilla, named Snowflake, was a male wild born individual from Equatorial Guinea who lived at the Barcelona Zoo for almost 40 years. He was diagnosed with non-syndromic oculocutaneous albinism, i.e. white hair, light eyes, pink skin, photophobia and reduced visual acuity. Despite previous efforts to explain the genetic cause, this is still unknown. Here, we study the genetic cause of his albinism and making use of whole genome sequencing data we find a higher inbreeding coefficient compared to other gorillas.
We successfully identified the causal genetic variant for Snowflake’s albinism, a non-synonymous single nucleotide variant located in a transmembrane region of SLC45A2. This transporter is known to be involved in oculocutaneous albinism type 4 (OCA4) in humans. We provide experimental evidence that shows that this amino acid replacement alters the membrane spanning capability of this transmembrane region. Finally, we provide a comprehensive study of genome-wide patterns of autozygogosity revealing that Snowflake’s parents were related, being this the first report of inbreeding in a wild born Western lowland gorilla.
In this study we demonstrate how the use of whole genome sequencing can be extended to link genotype and phenotype in non-model organisms and it can be a powerful tool in conservation genetics (e.g., inbreeding and genetic diversity) with the expected decrease in sequencing cost.
Gorilla; Albinism; Inbreeding; Genome; Conservation
Ancient DNA has revolutionized conservation genetic studies as it allows monitoring of the genetic variability of species through time and predicting the impact of ecosystems’ threats on future population dynamics and viability. Meanwhile, the consequences of anthropogenic activities and climate change to island faunas, particularly seabirds, remain largely unknown. In this study, we examined temporal changes in the genetic diversity of a threatened seabird, the Cory’s shearwater (Calonectris borealis).
We analysed the mitochondrial DNA control region of ancient bone samples from the late-Holocene retrieved from the Canary archipelago (NE Atlantic) together with modern DNA sequences representative of the entire breeding range of the species. Our results show high levels of ancient genetic diversity in the Canaries comparable to that of the extant population. The temporal haplotype network further revealed rare but recurrent long-distance dispersal between ocean basins. The Bayesian demographic analyses reveal both regional and local population size expansion events, and this is in spite of the demographic decline experienced by the species over the last millennia.
Our findings suggest that population connectivity of the species has acted as a buffer of genetic losses and illustrate the use of ancient DNA to uncover such cryptic genetic events.
Ancient DNA; Population size; Calonectris
The developed cognitive capabilities for Homo sapiens seems to be the result of a specialized and lateralized brain, and as a result of this, humans display the highest degree of manual specialization or handedness among the primates. Studies regarding its emergence and distribution within the genus Homo show that handedness is present very early. The mode in which it was articulated and spread across the different species during the course of human evolution could provide information about our own cognitive capacities. Here we report the manual laterality attributed to eleven 49,000 old Neandertal individuals from El Sidrón cave (Spain), through the study of instrumental or cultural striations on the anterior dentition. Our results show a predominant pattern addressed to right-handers. These results fit within the modern human handedness distribution pattern and provide indirect evidence for behavior and brain lateralization on Neandertals. They support the early establishment of handedness in our genus. Moreover, the individual identified as Juvenile 1 (6–8 years old at death), displays the same striation pattern as the adult Neandertals from the sample, and thereby the ontogenic development of manual laterality in that Neandertal population seems to be similar to that of living modern humans.
The arrival of agriculture into Europe during the Neolithic transition brought a significant shift in human lifestyle and subsistence. However, the conditions under which the spread of the new culture and technologies occurred are still debated. Similarly, the roles played by women and men during the Neolithic transition are not well understood, probably due to the fact that mitochondrial DNA (mtDNA) and Y chromosome (NRY) data are usually studied independently rather than within the same statistical framework. Here, we applied an integrative approach, using different model-based inferential techniques, to analyse published datasets from contemporary and ancient European populations. By integrating mtDNA and NRY data into the same admixture approach, we show that both males and females underwent the same admixture history and both support the demic diffusion model of Ammerman and Cavalli-Sforza. Similarly, the patterns of genetic diversity found in extant and ancient populations demonstrate that both modern and ancient mtDNA support the demic diffusion model. They also show that population structure and differential growth between farmers and hunter-gatherers are necessary to explain both types of data. However, we also found some differences between male and female markers, suggesting that the female effective population size was larger than that of the males, probably due to different demographic histories. We argue that these differences are most probably related to the various shifts in cultural practices and lifestyles that followed the Neolithic Transition, such as sedentism, the shift from polygyny to monogamy or the increase of patrilocality.
Only a few genetic studies have been carried out to date in Bolivia. However, some of the most important (pre)historical enclaves of South America were located in these territories. Thus, the (sub)-Andean region of Bolivia was part of the Inca Empire, the largest state in Pre-Columbian America. We have genotyped the first hypervariable region (HVS-I) of 720 samples representing the main regions in Bolivia, and these data have been analyzed in the context of other pan-American samples (>19,000 HVS-I mtDNAs). Entire mtDNA genome sequencing was also undertaken on selected Native American lineages. Additionally, a panel of 46 Ancestry Informative Markers (AIMs) was genotyped in a sub-set of samples. The vast majority of the Bolivian mtDNAs (98.4%) were found to belong to the main Native American haplogroups (A: 14.3%, B: 52.6%, C: 21.9%, D: 9.6%), with little indication of sub-Saharan and/or European lineages; however, marked patterns of haplogroup frequencies between main regions exist (e.g. haplogroup B: Andean [71%], Sub-Andean [61%], Llanos [32%]). Analysis of entire genomes unraveled the phylogenetic characteristics of three Native haplogroups: the pan-American haplogroup B2b (originated ∼21.4 thousand years ago [kya]), A2ah (∼5.2 kya), and B2o (∼2.6 kya). The data suggest that B2b could have arisen in North California (an origin even in the north most region of the American continent cannot be disregarded), moved southward following the Pacific coastline and crossed Meso-America. Then, it most likely spread into South America following two routes: the Pacific path towards Peru and Bolivia (arriving here at about ∼15.2 kya), and the Amazonian route of Venezuela and Brazil southwards. In contrast to the mtDNA, Ancestry Informative Markers (AIMs) reveal a higher (although geographically variable) European introgression in Bolivians (25%). Bolivia shows a decreasing autosomal molecular diversity pattern along the longitudinal axis, from the Altiplano to the lowlands. Both autosomes and mtDNA revealed a low impact (1–2%) of a sub-Saharan component in Bolivians.
The necrophagous burying beetle Nicrophorus vespilloides reproduces on small carcasses that are buried underground to serve as food for their offspring. Cadavers that are too large to bury have previously been postulated to be important food sources for newly emerged beetles; however, the attractiveness of distinct successive stages of decomposition were not further specified. Therefore, we investigated the potential preference of newly emerged N. vespilloides females for odour bouquets of piglet cadavers at specific stages of decomposition. Analyses of walking tracks on a Kramer sphere revealed a significantly higher mean walking speed and, consequently, a higher mean total track length when beetles were confronted with odour plumes of the decomposition stages ‘post-bloating’, ‘advanced decay’ or ‘dry remains’ in comparison with the solvent control. Such a change of the walking speed of newly emerged N. vespilloides females indicates a higher motivation to locate such food sources. In contrast to less discriminating individuals this behaviour provides the advantage of not wasting time at unsuitable food sources. Furthermore, in the advanced decay stage, we registered a significantly higher preference of beetles for upwind directions to its specific odour plume when compared with the solvent control. Such a change to upwind walking behaviour increases the likelihood that a large cadaver will be quickly located. Our findings are of general importance for applied forensic entomology: newly emerged N. vespilloides females on large cadavers can and should be regarded as potential indicators of prolonged post mortem intervals as our results clearly show that they prefer emitted odour bouquets of later decomposition stages.
Kuhl’s pipistrelle is found from Europe and North Africa all of the way to Asia, yet studies have thus far concentrated on the western limit of its distribution. Here we form a multi-marker picture of the diversity of Kuhl’s pipistrelle at a mid point in the Arabian peninsula in an attempt to redress the western sampling bias and to represent a region from which no genetic data has thus far been presented for this species. The three Arabian Cytochrome b haplotypes showed a clear divergence of 19 substitutions from those found in either Europe or North Africa. Molecular dating suggests the Arabian population split from the remaining Kuhl’s somewhere between 0.7 and 1.7 million years before present around the time of a series of aridification events across northern Africa. Well supported lineages within Arabia are typical of that which may be seen after an expansion from multiple Pleistocene refugia, but may also reflect the loss of intermediate haplotypes during historical population fluctuations. A long-term population contraction coincides with climatic changes towards those conditions more typical of contemporary Arabia.
The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy’s zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further characterize the complete mitochondrial genomes of three extinct equid lineages (the New World stilt-legged horses, NWSLH; the subgenus Sussemionus; and the Quagga, Equus quagga quagga). Comparisons with extant taxa confirm the NWSLH as being part of the caballines, and the Quagga and Plains zebras as being conspecific. However, the evolutionary relationships among the non-caballine lineages, including the now-extinct subgenus Sussemionus, remain unresolved, most likely due to extremely rapid radiation within this group. The closest living outgroups (rhinos and tapirs) were found to be too phylogenetically distant to calibrate reliable molecular clocks. Additional mitochondrial genome sequence data, including radiocarbon dated ancient equids, will be required before revisiting the exact timing of the lineage radiation leading up to modern equids, which for now were found to have possibly shared a common ancestor as far as up to 4 Million years ago (Mya).
Among the winged insects (Pterygota) the Dragonflies and Damselflies (Odonata) are unique for several reasons. Behaviourally they are aerial predators that hunt and catch their prey in flight, only. Morphologically the flight apparatus of Odonata is significantly different from what is found in the remaining Pterygota. However, to understand the phylogenetic relationships of winged insects and the origin and evolution of insect flight in general, it is essential to know how the elements of the odonatan flight apparatus relate to those of the other Pterygota. Here we present a comprehensive, comparative morphological investigation of the thoracic flight musculature of damselflies (Zygoptera). Based on our new data we propose a homologization scheme for the thoracic musculature throughout Pterygota. The new homology hypotheses will allow for future comparative work and especially for phylogenetic analyses using characters of the thoracic musculature throughout all winged insects. This will contribute to understand the early evolution of pterygote insects and their basal phylogenetic relationship.
Island populations have been extensively used as model systems in ecology, biogeography, conservation and evolutionary biology, owing to the several simplifying assumptions that they allow. Nevertheless, recent findings from intra-island phylogeographic studies are casting doubts on the generality of some of these underlying assumptions. We investigated the phylogeography, historical demography, and population genetic structure of the Corsican endemic frog, Discoglossus montalentii. In contrast with expectations based on its insular, restricted and continuous distribution, we found evidence of 3 phylogroups, whose rather ancient divergence (Early-Middle Pleistocene) was likely primed by climatic changes that occurred during the ‘middle Pleistocene revolution’. Furthermore, their differentiation explained most (68%) of the overall genetic diversity that was observed. These results and the growing evidence from intra-island phylogeographies, suggest that island populations frequently may not conform to some long-standing assumptions, including long-term stability, range-wide panmixia and the correlation of effective population size to the island size. As a consequence, both for theoretical and for applied purposes, the extensive use of these assumptions in the study of island populations warrants a careful re-examination.
Bones, teeth and hair are often the only physical evidence of human or animal presence at an archaeological site; they are also the most widely used sources of samples for ancient DNA (aDNA) analysis. Unfortunately, the DNA extracted from ancient samples, already scarce and highly degraded, is widely susceptible to exogenous contaminations that can affect the reliability of aDNA studies. We evaluated the molecular effects of sample handling on five human skeletons freshly excavated from a cemetery dated between the 11 to the 14th century. We collected specimens from several skeletal areas (teeth, ribs, femurs and ulnas) from each individual burial. We then divided the samples into two different sets: one labeled as “virgin samples” (i.e. samples that were taken by archaeologists under contamination-controlled conditions and then immediately sent to the laboratory for genetic analyses), and the second called “lab samples”(i.e. samples that were handled without any particular precautions and subject to normal washing, handling and measuring procedures in the osteological lab). Our results show that genetic profiles from “lab samples” are incomplete or ambiguous in the different skeletal areas while a different outcome is observed in the “virgin samples” set. Generally, all specimens from different skeletal areas in the exception of teeth present incongruent results between “lab” and “virgin” samples. Therefore teeth are less prone to contamination than the other skeletal areas we analyzed and may be considered a material of choice for classical aDNA studies. In addition, we showed that bones can also be a good candidate for human aDNA analysis if they come directly from the excavation site and are accompanied by a clear taphonomic history.
Species in the ivesioid clade of Potentilla (Rosaceae) are endemic to western North America, an area that underwent widespread aridification during the global temperature decrease following the Mid-Miocene Climatic Optimum. Several morphological features interpreted as adaptations to drought are found in the clade, and many species occupy extremely dry habitats. Recent phylogenetic analyses have shown that the sister group of this clade is Potentilla section Rivales, a group with distinct moist habitat preferences. This has led to the hypothesis that the ivesioids (genera Ivesia, Horkelia and Horkeliella) diversified in response to the late Tertiary aridification of western North America. We used phyloclimatic modeling and a fossil-calibrated dated phylogeny of the family Rosaceae to investigate the evolution of the ivesioid clade. We have combined occurrence- and climate data from extant species, and used ancestral state reconstruction to model past climate preferences. These models have been projected into paleo-climatic scenarios in order to identify areas where the ivesioids may have occurred. Our analysis suggests a split between the ivesioids and Potentilla sect. Rivales around Late Oligocene/Early Miocene (∼23 million years ago, Ma), and that the ivesioids then diversified at a time when summer drought started to appear in the region. The clade is inferred to have originated on the western slopes of the Rocky Mountains from where a westward range expansion to the Sierra Nevada and the coast of California took place between ∼12-2 Ma. Our results support the idea that climatic changes in southwestern North America have played an important role in the evolution of the local flora, by means of in situ adaptation followed by diversification.
The Réunion grey white-eye (Zosterops borbonicus) is a single-island endemic passerine bird that exhibits striking geographically structured melanic polymorphism at a very small spatial scale. We investigated the genetic basis of this color polymorphism by testing whether the melanocortin-1 receptor (MC1R), a gene often involved in natural melanic polymorphism in birds, was associated with the observed plumage variation. Although we found three non-synonymous mutations, we detected no association between MC1R variants and color morphs, and the main amino-acid variant found in the Réunion grey white-eye was also present at high frequency in the Mauritius grey white-eye (Zosterops mauritianus), its sister species which shows no melanic polymorphism. In addition, neutrality tests and analysis of population structure did not reveal any obvious pattern of positive or balancing selection acting on MC1R. Altogether these results indicate that MC1R does not play a role in explaining the melanic variation observed in the Réunion grey white-eye. We propose that other genes such as POMC, Agouti or any other genes involved in pigment synthesis will need to be investigated in future studies if we are to understand how selection shapes complex patterns of melanin-based plumage pigmentation.
All sequences submitted to Genbank. Accession number: JX914505 to JX914564.
Hunter-gatherers living in Europe during the transition from the late Pleistocene to the Holocene intensified food acquisition by broadening the range of resources exploited to include marine taxa. However, little is known on the nature of this dietary change in the Mediterranean Basin. A key area to investigate this issue is the archipelago of the Ègadi Islands, most of which were connected to Sicily until the early Holocene. The site of Grotta d’Oriente, on the present-day island of Favignana, was occupied by hunter-gatherers when Postglacial environmental changes were taking place (14,000-7,500 cal BP). Here we present the results of AMS radiocarbon dating, palaeogenetic and isotopic analyses undertaken on skeletal remains of the humans buried at Grotta d’Oriente. Analyses of the mitochondrial hypervariable first region of individual Oriente B, which belongs to the HV-1 haplogroup, suggest for the first time on genetic grounds that humans living in Sicily during the early Holocene could have originated from groups that migrated from the Italian Peninsula around the Last Glacial Maximum. Carbon and nitrogen isotope analyses show that the Upper Palaeolithic and Mesolithic hunter-gatherers of Favignana consumed almost exclusively protein from terrestrial game and that there was only a slight increase in marine food consumption from the late Pleistocene to the early Holocene. This dietary change was similar in scale to that at sites on mainland Sicily and in the rest of the Mediterranean, suggesting that the hunter-gatherers of Grotta d’Oriente did not modify their subsistence strategies specifically to adapt to the progressive isolation of Favignana. The limited development of technologies for intensively exploiting marine resources was probably a consequence both of Mediterranean oligotrophy and of the small effective population size of these increasingly isolated human groups, which made innovation less likely and prevented transmission of fitness-enhancing adaptations.
The Cheiruridae are a diverse group of trilobites and several subfamilies within the clade have been the focus of recent phylogenetic studies. This paper focuses on the relationships of one of those subfamilies, the Ordovician Eccoptochilinae. We analyze sixteen species from six genera within the traditionally defined group, using the pilekiid Anacheirurus frederici as an outgroup. To assess the monophyly of the Eccoptochilinae seven sphaerexochine species, Kawina arnoldi, Sphaerexochus arenosus, S. atacius, S. latifrons, S. mirus, S. parvus, and S. scabridus were included in the analysis as well. The results of this analysis show that the genus Eccoptochile represents a paraphyletic grade and species traditionally assigned to Parasphaerexochus and Skelipyx plot within Pseudosphaerexochus. Also, representative species of Sphaerexochinae plot within the traditionally defined Eccoptochilinae, suggesting Eccoptochilinae itself is paraphyletic. To resolve this, we propose all species of Pseudosphaerexochus be placed within Sphaerexochinae and Eccoptochilinae be restricted to a monotypic Eccoptochile clavigera.
A recent discovery of Iron Age burials (Pazyryk culture) in the Altai Mountains of Mongolia may shed light on the mode and tempo of the generation of the current genetic east-west population admixture in Central Asia. Studies on ancient mitochondrial DNA of this region suggest that the Altai Mountains played the role of a geographical barrier between West and East Eurasian lineages until the beginning of the Iron Age. After the 7th century BC, coinciding with Scythian expansion across the Eurasian steppes, a gradual influx of East Eurasian sequences in Western steppes is detected. However, the underlying events behind the genetic admixture in Altai during the Iron Age are still unresolved: 1) whether it was a result of migratory events (eastward firstly, westward secondly), or 2) whether it was a result of a local demographic expansion in a ‘contact zone’ between European and East Asian people. In the present work, we analyzed the mitochondrial DNA lineages in human remains from Bronze and Iron Age burials of Mongolian Altai. Here we present support to the hypothesis that the gene pool of Iron Age inhabitants of Mongolian Altai was similar to that of western Iron Age Altaians (Russia and Kazakhstan). Thus, this people not only shared the same culture (Pazyryk), but also shared the same genetic east-west population admixture. In turn, Pazyryks appear to have a similar gene pool that current Altaians. Our results further show that Iron Age Altaians displayed mitochondrial lineages already present around Altai region before the Iron Age. This would provide support for a demographic expansion of local people of Altai instead of westward or eastward migratory events, as the demographic event behind the high population genetic admixture and diversity in Central Asia.
Archaeologists interested in explaining changes in artifact morphology over long time periods have found it useful to create models in which the only source of change is random and unintentional copying error, or ‘cultural mutation’. These models can be used as null hypotheses against which to detect non-random processes such as cultural selection or biased transmission. One proposed cultural mutation model is the accumulated copying error model, where individuals attempt to copy the size of another individual's artifact exactly but make small random errors due to physiological limits on the accuracy of their perception. Here, we first derive the model within an explicit mathematical framework, generating the predictions that multiple independently-evolving artifact chains should diverge over time such that their between-chain variance increases while the mean artifact size remains constant. We then present the first experimental test of this model in which 200 participants, split into 20 transmission chains, were asked to faithfully copy the size of the previous participant's handaxe image on an iPad. The experimental findings supported the model's prediction that between-chain variance should increase over time and did so in a manner quantitatively in line with the model. However, when the initial size of the image that the participants resized was larger than the size of the image they were copying, subjects tended to increase the size of the image, resulting in the mean size increasing rather than staying constant. This suggests that items of material culture formed by reductive vs. additive processes may mutate differently when individuals attempt to replicate faithfully the size of previously-produced artifacts. Finally, we show that a dataset of 2601 Acheulean handaxes shows less variation than predicted given our empirically measured copying error variance, suggesting that other processes counteracted the variation in handaxe size generated by perceptual cultural mutation.
One of the main findings derived from the analysis of the Neandertal genome was the evidence for admixture between Neandertals and non-African modern humans. An alternative scenario is that the ancestral population of non-Africans was closer to Neandertals than to Africans because of ancient population substructure. Thus, the study of North African populations is crucial for testing both hypotheses. We analyzed a total of 780,000 SNPs in 125 individuals representing seven different North African locations and searched for their ancestral/derived state in comparison to different human populations and Neandertals. We found that North African populations have a significant excess of derived alleles shared with Neandertals, when compared to sub-Saharan Africans. This excess is similar to that found in non-African humans, a fact that can be interpreted as a sign of Neandertal admixture. Furthermore, the Neandertal's genetic signal is higher in populations with a local, pre-Neolithic North African ancestry. Therefore, the detected ancient admixture is not due to recent Near Eastern or European migrations. Sub-Saharan populations are the only ones not affected by the admixture event with Neandertals.