Article

Molecular systematics and phylogeography of the genus Alburnus Rafinesque, 1820 (Teleostei, Leuciscidae) in Turkey

Authors:
  • Recep Tayyip Erdogan University
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Abstract

In this study, the phylogeny of Alburnus genus distributed in Turkish freshwaters was performed by analyzing mitochondrial cyt b gene (1141 bp) and COI gene (1551 bp) sequences from 1172 samples representing 112 populations of 24 species through their geographical distribution. According to our findings, 20 valid species are distributed in Turkey of which 18 have already been known. While six Alburnus species (A. battalgilae, A. istanbulensis, A. carinatus, A. schischkovi, A. nasreddini ve A. adanensis) have been synonomized, two new species (Alburnus sp.1 and Alburnus sp.2) from Dicle River and Çapraz Stream/Susurluk River have been identified. Extinct species such as A. akili and A. nicaeensis have not been observed in situ. Phylogenetic tree topologies and haplotype network of the 119 cyt b and 80 COI haplotypes detected in Alburnus species have indicated a consensus tree topology containing twenty lineages, each of corresponding to one species, and three Alburnus haplogroups corresponding to the geographical origins: Eastern Anatolia (I), Mediterranean (2) and Western & Northern Anatolia (3). The results indicate that the divergence between those haplogroups may have occurred during the Middle Miocene-Middle Pleistocene periods (from 14.9 to 5.29 million years).

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... Two species were recently added to the long synonymy of A. sellal: Alburnus selcuklui described by Elp et al. (2015) from the Botan basin, a tributary to the upper Tigris in Turkey, and Alburnus zagrosensis described by Coad (2009) from the Karun basin, a tributary to the lower Tigris in Iran (see Freyhof et al., 2018, andEagderi et al., 2019, respectively). In their phylogenetic analyses of 112 populations of 24 species of Alburnus in Turkey using two mitochondrial genes (COI and cyt b), Bektaş et al. (2020) also supported the synonymization of A. selcuklui with A. sellal. The same study identified two potentially new species of Alburnus. ...
... Freyhof et al. (2018) discovered that A. heckeli and A. sellal sometimes shared the same DNA barcode sequence (COI) and the two species cannot be distinguished based on such molecular data. This was corroborated by Bektaş et al. (2020) who calculated that the genetic distance between A. heckeli and A. sellal was 1.74 for cyt b and only 0.34 for COI. Alburnus heckeli and A. sellal were closely related sister taxa based on COI, and grouped together with A. tarichi (endemic to endorheic Lake Van) and Alburnus sp. 1 (upper Tigris basin) based on cyt b (Bektaş et al., 2020). ...
... This was corroborated by Bektaş et al. (2020) who calculated that the genetic distance between A. heckeli and A. sellal was 1.74 for cyt b and only 0.34 for COI. Alburnus heckeli and A. sellal were closely related sister taxa based on COI, and grouped together with A. tarichi (endemic to endorheic Lake Van) and Alburnus sp. 1 (upper Tigris basin) based on cyt b (Bektaş et al., 2020). ...
Article
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... Being located at the intersection of bordering areas, with distinct evolutionary origins and varied ecological and geographical environments, this region provided a high potential for faunal interchanges, especially over the last 24 million years. The evolution of the hydrographic networks that changed considerably from the Miocene until the present day, turned the Eastern Mediterranean into a region of high diversity and endemism of freshwater taxa such as fish and gastropods (Heller, 2007;Bektas et al., 2019Bektas et al., , 2020. However, the phylogeography of the freshwater mussels from this area is poorly understood, hampering the evaluation of biogeographic hypotheses. ...
... The colonization of Western Anatolia by Unio pictorum sensu stricto possibly occurred in two main waves of range expansion from central Europe (Figs. 1 and 3). The first was in the Pleistocene, possibly through the series of freshwater lakes that connected Western Anatolia and Greece (Krijgsman et al., 2020) and then a post-glacial second wave via the Black Sea coastal route (Bektas et al., 2020). While the ancient distribution expansion can be seen in the divergent haplotypes of the Greek populations and the Rivers Maritsa and the closely related species Unio eucirrus from River Karamenderes in Turkey, the recent invasion is evident in the related or shared haplotypes of the remaining populations in Anatolia with those from Central Europe (Fig. 3). ...
... This system was then formed by the Late Miocene (Demir et al., 2007;Stow et al., 2020). The freshwater mussel faunal interchanges of the Euphrates with the Orontes, can be explained by the formation of a patchwork of connections 6,000 years ago (Por and Dimentman, 1985), but this event still needs further research (Bektas et al., 2020). The River Orontes, having the highest density of fish endemism in the Mediterranean, also had past faunal connections with rivers Seyhan, Ceyhan, and Jordan (Por and Dimentman, 1985), explaining the distribution of Unio delicatus, U. damascensis, Potomida semirugata, and the southern Anatolian Anodonta anatina lineage. ...
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Located at the junction between Europe, Africa, and Asia, with distinct evolutionary origins and varied ecological and geographical settings, together with a marked history of changes in orogeny and configuration of the main river basins, turned the Eastern Mediterranean into a region of high diversity and endemism of freshwater taxa. Freshwater mussels (Bivalvia, Unionidae) from the Western Palearctic have been widely studied in their European range, but little attention has been dedicated to these taxa in the Eastern Mediterranean region and their diversity and phylogeography are still poorly understood. The present study aims to resolve the diversity, biogeography, and evolutionary relationships of the Eastern Mediterranean freshwater mussels. To that end, we performed multiple field surveys, phylogenetic analyses, and a thorough taxonomic revaluation. We reassessed the systematics of all Unionidae species in the region, including newly collected specimens across Turkey, Israel, and Iran, combining COI + 16S + 28S and COI phylogenies with molecular species delineation methods. Phylogeographical patterns were characterized based on published molecular data, newly sequenced specimens, and species distribution data, as well as ancestral range estimations. We reveal that Unionidae species richness in the Eastern Mediterranean is over 70% higher than previously assumed, counting 19 species within two subfamilies, the Unioninae (14) and Gonideinae (5). We propose two new species, Anodonta seddoni sp. nov. and Leguminaia anatolica sp. nov. Six additional taxa, Unio delicatus stat. rev., Unio eucirrus stat. rev., Unio hueti stat. rev., Unio sesirmensis stat. rev., Unio terminalis stat. rev. removed from the synonymy of Unio tigridis, as well as Unio damascensis stat. rev. removed from the synonymy of Unio crassus, are re-described. The nominal taxa Unio rothi var. komarowi O. Boettger, 1880 and Unio armeniacus Kobelt, 1911 are proposed as new synonyms of Unio bruguierianus, and Anodonta cyrea Drouët, 1881 and Anodonta cilicica Kobelt & Rolle, 1895 as new synonyms of Anodonta anatina. Also, the presence of Unio tumidus in the Maritza River is confirmed. The phylogeographic patterns described here are interpreted concerning major past geological events. Conservation needs and implications are presented, together with populations and species conservation priorities.
... Due to the location at the crossroads of neighbouring regions with varying ecological and geographical characteristic, Türkiye's freshwater fish species have high diversity and endemism (Hrbek et al., 2004;Perea et al., 2010;Çiçek et al., 2018;Bektaş et al., 2020). According to the present ichthyofauna, Türkiye is inhabited by 384 species of freshwater fish, 208 of which are endemic (Çiçek et al., 2020). ...
... According to the present ichthyofauna, Türkiye is inhabited by 384 species of freshwater fish, 208 of which are endemic (Çiçek et al., 2020). The Alburnus genus has 24 species in Türkiye, 17 of which are endemic to Türkiye (Bektaş et al, 2020;Çiçek et al., 2020), while the genus has 48 species worldwide (Froese & Pauly, 2022). The species Alburnus istanbulensis (Battalgil, 1941) is one of the endemic species in Türkiye. ...
... Alburnus sellal Heckel, 1843 from the Cyprinidae family has a wide distribution area in Turkey. According to some molecular systematic and phylogeographic studies conducted in recent years (Mohammadian-Kalat et al. 2017;Bektaş et al. 2020;Çiçek et al. 2020;Jouladeh-Roudbar et al. 2020;Freyhof et al. 2021), Alburnus mossulensis Heckel, 1843 described from the Euphrates-Tigris River System was revised and reported as a synonym of A. sellal Heckel, 1843 (Düşükcan et al. 2022). ...
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In this study, predictions were made on the growth performance of Alburnus sellal Heckel, 1843 from the Munzur River using back propagation artificial neural networks and ANN algorithms. Statistical growth models used in fish biology and results obtained from artificial neural networks were compared. A total of 239 samples were used in this comparison. It was determined that the population is distributed across age groups 0–VII. The relationship between length and weight was calculated as W = 0.0046L3.198 for all individuals. The von Bertalanffy growth parameters were calculated for all individuals: Lt = 21.93 [1 – e–0.158 (t + 2.11)]; Wt = 102.29 [1 – e–0.158 (t + 2.11)] 3.198. The growth performance index (Ф’) value was 1.880 for all individuals. The condition factor varied between 0.479 and 1.115 for females and between 0.533 and 1.076 for males. The Mean Absolute Percent Error (MAPE) statistic was used, which is a widely used method to measure the accuracy of the predictions made. It was determined that ANNs MAPE (%) values were better than MAPE values calculated for the length–weight relationship and von Bertalanffy growth function models for A. sellal. This study shows that ANNs can be used as an alternative useful method for predicting population parameters. ANN models are therefore an effective tool to describe fish growth parameters. They have been found to be a useful predictive tool. The developed models can be used to predict future sustainable fish management.
... The geography of Türkiye has become the hub for diversifying many species and taxa currently recognized. Recent genetic-based studies on this topic demonstrate Türkiye's contribution to the planet's biodiversity (Geiger et al. 2014;Bektaş et al. 2019Bektaş et al. , 2020. Despite this rich biodiversity, the genus Phoxinus does not have a wide distribution in Türkiye. ...
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Phoxinus radeki , a new species, is described from the Ergene River (Aegean Sea Basin). It is distinguished from Phoxinus species in Türkiye and the adjacent area by having the scales of the breast, scaled but separated unscaled area anteriorly, short dark rectangular blotches along the lateral line between the lateral line and belly yellowish in both males and females, body depth dorsal fin origin 16–21% SL, caudal peduncle depth 8–10% SL. Additionally, molecular results demonstrated that the new species differed from its closest congeners with a mean genetic distance value of 3.08% (min. 2.82–max. 3.29) and moderately support values in cytochrome b (Cyt b ) gene partial sequences (1064 bp.). Further, the species delimitation analysis identified the new species as a single MOTU independent of other Phoxinus species.
... Based on the results of the genetic analysis, the two couples of Alburnus species mentioned above could be merged into two single species. However, since other studies have observed low genetic distance between some species of the genus Alburnus [73,74], further study of these species through nuclear or faster evolving genetic markers could help define their status more accurately. ...
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Biodiversity is a key factor for the functioning and efficiency of an ecosystem. Greece, though covering a relatively small surface area, hosts a great deal of species diversity. This is especially true for freshwater fishes. In recent years, the traditional methods of species identification have been supplemented by the use of molecular markers. The present study therefore aims to extensively produce DNA barcodes for Greek freshwater fish species and investigate thoroughly if the presently accepted species classification is in agreement with molecular data. A 624-bases long fragment of the COI gene was sequenced, from 406 freshwater fish specimens belonging to 24 genera and originating from 18 lake and river sites. These sequences were used along with 596 sequences from the same genera, recovered from BOLD, for the construction of phylogenetic trees and the estimation of genetic distances between individuals. In total, 1002 sequences belonging to 72 species were analyzed. The method was found to be effective for 55 of 72 studied species. 17 closely related species with low interspecific genetic distances were observed, for which further study is proposed. It should also be noted that, in four cases, cryptic diversity was observed, where groups originally identified as one species exhibited genetic distance great enough to be separated into discrete species. Region specific haplotypes were also detected within populations of 14 species, giving the possibility to identify even the geographic origin of a species. Our findings are discussed in the light of the rich history of the Balkan peninsula and provide a significant steppingstone for the further study of Greek and European freshwater fish biodiversity.
... According to IUCN Red List, it was assessed as endangered species, with a decreasing population trend (Barrios et al. 2014;Innal and Giannetto 2020). The Antalya bleak was studied concerning the morphometric measurements (Mangit, 2014), age and growth parameters (Innal and Gülle 2019) or phylogeography (Bektas et al. 2020), however with respect to ichthyoparasitofauna, data remain scarce. The copepod Lernaea cyprinacea was detected before on A. baliki in Karpuzçay Creek (Innal, 2020). ...
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Lernaeid copepod Lernaea cyprinacea L., 1758 has been reported on the skin and the external surfaces of fins from three freshwater fish hosts: endemic species Alburnus baliki Bogutskaya, Küçük & Ünlü, 2000 and Pomatoschistus anatoliae Engin & Innal, 2017 and on native species Chelon ramada Risso, 1827 sampled from Karpuzçay Creek Estuary, located in the Mediterranean region of Turkey. The highest prevalence of infection (7.5%) was reached in C. ramada, and the mean intensity was the same (1 parasite/fish) in all three host species. P. anatoliae (Gobiiformes: Gobiidae) was found as new host record for ectoparasite L. cyprinacea. Histopathological examination of the sections made in all analyzed fish hosts revealed chronic granulomatous inflammatory reaction and infiltration of lymphocytes, histiocytes and eosinophils around the parasite attachment sites
... Most of the Leuciscidae species belong to the Alburnus (9 species) and Pseudophoxinus (9 species) genera (72% in total). Alburnus was found to be very rich in Turkey, with 20 valid species reported to occur in the country [46,47]. Hrbek et al. [48] underlined the significant role of central Anatolian plate tectonic events on the diversification and phylogenetic relationships of the genus Pseudophoxinus, which is often co-distributed with Anatolichthys (Aphaniidae) in Central Anatolia. ...
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Due to its peculiar geographical position and its environmental heterogeneity, Turkey represents an important biodiversity hotspot for freshwater fish fauna. Unfortunately, native fish communities of Turkey, mainly from lentic ecosystems, have been massively altered in the past decades. Furthermore, these species, especially the endemic species, are now threatened by several human activities in addition to the global issue of climatic changes. The aim of this paper is to provide an updated review on the current status of endemic fish species from main lakes of Turkey including major threats affecting fish assemblages. By gathering data from the literature and authors’ personal observations, 62 endemic fish species were reported to occur in the considered 37 Turkish Lakes. The presence of non-native species, agriculture activities, climatic drought, and decreasing water level were found to be the threats that most affect the fish communities of the considered Turkish Lakes.
... Based on molecular data, Mangit and Yerli (2018) reported that there were 21 valid species in freshwaters of Turkey. The latest study on this genus was conducted by Bektaş et al. (2020). This study identified the substantial Alburnus species in Turkey and clarified their interspecific relationships by using the entire cyt b and the coI gene sequences. ...
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... Freyhof et al. (2018b) accepted A. adanensis as a valid species and suggested that it might be extinct. Finally, Bektaş et al. (2020) have studied molecular characters of the genus Alburnus, and they recently treat as a synonym of A. kotschy. ...
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This study was carried out to determine the fish species of Van Lake Basin between in 2008-2012. Van Lake Basin is a closed basin that shaped approximately 2.3 % of Turkey. Because of closed basin character, the differences indicated in species diversity. Basin is rich in endemic species diversity with plant and animal species. This richness were reflected to fish species. All of the fish species naturally occurring in the lake basin are consist of endemic species. Alburnus tarichi, Alburnus timarensis, Barbus ercisianus, Capoeta cosswigi and Oxynoemacheilus ercisianus exhibited a natural distribution. Cyprinus carpio, Carassius gibelio, Gambusia holbrooki and Aphanius mento were constituted population from various water sources. In addition, escaped from fish farm sorvaccinated to water resources Oncorhynchus mykiss was unable to create the population. Barbus ercisianus and Capoeta cosswigi shown to create hybrid fish species in Zilan and Deliçay. Cyprinus carpio and Carassius carassius shown to create hybrid fish species in Nazik Lake.
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This study was carried out to determine the fish species of Van Lake Basin between in 2008- 2012. Van Lake Basin is a closed basin that shaped approximately 2.3 % of Turkey. Because of closed basin character, the differences indicated in species diversity. Basin is rich in endemic species diversity with plant and animal species. This richness were reflected to fish species. All of the fish species naturally occurring in the lake basin are consist of endemic species. Alburnus tarichi, Alburnus timarensis, Barbus ercisianus, Capoeta cosswigi and Oxynoemacheilus ercisianus exhibited a natural distribution. Cyprinus carpio, Carassius gibelio, Gambusia holbrooki and Aphanius mento were constituted population from various water sources. In addition, escaped from fish farm sorvaccinated to water resources Oncorhynchus mykiss was unable to create the population. Barbus ercisianus and Capoeta cosswigi shown to create hybrid fish species in Zilan and Deliçay. Cyprinus carpio and Carassius carassius shown to create hybrid fish species in Nazik Lake.
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The Tethysides are a superorogenic complex flanking the Eurasian continent to the south and consisting of the Cimmerides and Alpides, products of Palaeo- and Neo-Tethys respectively. We here review their evolution, mainly on the basis of new maps showing the distribution of sutures, magmatic rocks, certain palaeobiogeographically and palaeoclimatologically significant taxa and facies, and fragments of Pan-African (900-450 Ma) orogenic system forming the basement of many Tethyside blocks. These are supplemented by palaeomagnetic data reported in the literature. A fundamental tenet of this paper is that major sutures which contain ophiolite fragments, represent tectonic sections between continental blocks where oceanic crust has been subducted. Palaeo-Tethys came into existence largely in late Carboniferous time. Coevally, it began to be consumed by both internal and peripheral subduction zones, which continued into the Permian; some of these had been inherited from pre-Tethyan times. In the later Permian, rifting subparallel with the northern margin of Gondwana Land began between the Zagros and Malaysia, separating a Cimmerian continent from N. Gondwana Land, and thus heralding the opening of Neo-Tethys and other smaller oceans that were back-arc basins of Palaeo-Tethys. This rifting possibly also extended farther west into Crete and mainland Greece. However, the North China block, Yangtze block, Huanan block, the eastern moity of the Qangtang block (North Tibet), and Annamia, all originally pieces of the end-Proterozoic-early Palaeozoic Gondwana Land, had already separated from it in pre-late Carboniferous times, possibly during the Devonian. All of these blocks, and the Cimmerian continent, were characterized by Cathaysian floral elements in late Palaeozoic time. Palaeomagnetic and palaeontological data showing the original Gondwana Land affinity of these continental blocks are supplemented by correlating late Proterozoic-early Palaeozoic Pan-African sutures, orogenic belts, and sedimentary basin fragments across Tethyside sutures. Late Permian foraminiferal provinces are related to this palaeogeographical interpretation. By Triassic times, most Cimmeride subduction zones were already in existence. The Cimmerian Continent accelerated its separation from Gondwana Land and--locally in the late Permian-- began disintegrating internally along the Waser/Rushan-Pshart/Banggong Co-Nu Jiang/Mandalay ocean. By late Triassic time all of the Chinese blocks---except Lhasa--and Annamia had collided with each other and with Laurasia. The resulting enormous orogenic collage had a 'soft cushion' between itself and Laurasia, in the form of the enormous accretionary complex of the Songpan- Ganzi. This connection enabled Laurasian land vertebrates to reach south-east Asia by late Triassic time. In late Triassic to middle Jurassic times, most major Cimmeride collisions were completed. Widespread aridity in Central Asia occurred in late Jurassic time, probably in the rain shadow of the newly formed Cimmeride mountain wall. Neo-Tethyan subduction systems formed along the S. margin of the Cimmerides or within Neo- Tethyan oceanic lithosphere during the Jurassic. Most, if not all, were north- or east-dipping. They continued the northerly migration of the Tethyside blocks. Evolution of the Tethysides influenced the distribution of marine and terrestrial organisms, and affected sea-level changes and patterns of atmospheric circulation during much of the Mesozoic and Cainozoic. It is likely to have reflected the surface expression of a persistent trend in the largescale convective circulation in the mantle, that continuously transported material northward into the Tethyan domain.
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Phylogenies are usually dated by calibrating interior nodes against the fossil record. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, we contrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian total-evidence analysis. As a test case, we focus on the early radiation of the Hymenoptera, mostly documented by poorly preserved impression fossils that are difficult to place phylogenetically. Specifically, we compare node dating using nine calibration points derived from the fossil record with total-evidence dating based on 343 morphological characters scored for 45 fossil (4--20 complete) and 68 extant taxa. In both cases we use molecular data from seven markers (∼5 kb) for the extant taxa. Because it is difficult to model speciation, extinction, sampling, and fossil preservation realistically, we develop a simple uniform prior for clock trees with fossils, and we use relaxed clock models to accommodate rate variation across the tree. Despite considerable uncertainty in the placement of most fossils, we find that they contribute significantly to the estimation of divergence times in the total-evidence analysis. In particular, the posterior distributions on divergence times are less sensitive to prior assumptions and tend to be more precise than in node dating. The total-evidence analysis also shows that four of the seven Hymenoptera calibration points used in node dating are likely to be based on erroneous or doubtful assumptions about the fossil placement. With respect to the early radiation of Hymenoptera, our results suggest that the crown group dates back to the Carboniferous, ∼309 Ma (95% interval: 291--347 Ma), and diversified into major extant lineages much earlier than previously thought, well before the Triassic. [Bayesian inference; fossil dating; morphological evolution; relaxed clock; statistical phylogenetics.].
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Palaeorutilus enspelensis (Böhme 1996), the only fish species from the Upper Oligocene maar lake Enspel (Westerwald), is described and its phylogenetical position within the subfamily Phoxininae is discussed. The cladistic analysis of osteological and lepidological features indicates that the genusPalaeorutilus Gaudant 1988 is a member of the Chub Clade. Furthermore, including of the recent Eurasian taxaLagowskiella andEupallasella in the analysis, the Chub Clade can be divided into two monophyletic Clades: the EurasianPhoxinus Clade (including the holarcticPhoxinus) and the eastern North American Creek Chub Clade which includes the fossil genusPalaeorutilus as its basal sister taxon. These phylogenetical investigation as well as the recent and fossil distribution pattern of the Phoxininae support the following biogeographical hypothesis: The settlement of cyprinids in North America took place in several waves and different directions. The separation of Western Clade and Chub Clade did not occur in North America but in Eocene times in Asia. Members of the Creek Chub Clade migrated from Europe to eastern North America via a transatlantic route prior to the Middle Miocene.
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Probability models of branching processes and computer simulations of these models are used to examine stochastic survivorship of female lineages under a variety of demographic scenarios. A parameter II, defined as the probability of survival of two or more independent lineages over G generations, is monitored as a function of founding size of a population, population size at carrying capacity, and the frequency distributions of surviving progeny. Stochastic lineage extinction can be very rapid under certain biologically plausible demographic conditions. For stable-sized populations initiated by n females and/or regulated about carrying capacity k=n, it is highly probable that within about 4n generations all descendants will trace their ancestries to a single founder female. For a given mean family size, increased variance decreases lineage survivorship. In expanding populations, however, lineage extinction is dramatically slowed, and the final k value is a far more important determinant of II than is the size of the population at founding. The results are discussed in the context of recent empirical observations of low mitochondrial DNA (mtDNA) sequence heterogeneity in humans and expected distributions of asexually transmitted traits among sexually reproducing species.
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Computational evolutionary biology, statistical phylogenetics and coalescent-based population genetics are becoming increasingly central to the analysis and understanding of molecular sequence data. We present the Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package version 1.7, which implements a family of Markov chain Monte Carlo (MCMC) algorithms for Bayesian phylogenetic inference, divergence time dating, coalescent analysis, phylogeography and related molecular evolutionary analyses. This package includes an enhanced graphical user interface program called Bayesian Evolutionary Analysis Utility (BEAUti) that enables access to advanced models for molecular sequence and phenotypic trait evolution that were previously available to developers only. The package also provides new tools for visualizing and summarizing multispecies coalescent and phylogeographic analyses. BEAUti and BEAST 1.7 are open source under the GNU lesser general public license and available at http://beast-mcmc.googlecode.com and http://beast.bio.ed.ac.uk
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We reconstructed the matrilineal phylogeny of Asian algae-eating fishes of the genus Capoeta based on complete mitochondrial gene for cytochrome b sequences obtained from 20 species sampled from the majority of the range and 44 species of closely related barbs of the genera Barbus s. str. and Luciobarbus. The results of this study show that Capoeta forms a strongly supported monophyletic subclade nested within the Luciobarbus clade, suggesting that specialized scraping morphology appeared once in the evolutionary history of the genus. We detected three main groups of Capoeta: the Mesopotamian group, which includes three species from the Tigris-Euphrates system and adjacent water bodies, the Anatolian-Iranian group, which has the most diversified structure and encompasses many species distributed throughout Anatolian and Iranian inland waters, and the Aralo-Caspian group, which consists of species distributed in basins of the Caspian and Aral Seas, including many dead-end rivers in Central Asia and Northern Iran. The most probable origination pathway of the genus Capoeta is hypothesized to occur as a result of allopolyploidization. The origin of Capoeta was found around the Langhian-Serravallian boundary according to our molecular clock. The diversification within the genus occurred along Middle Miocene-Late Pliocene periods.
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The Oligocene-Miocene was a time characterized by major climate changes as well as changing plate configurations. The Middle Miocene Climate Transition (17 to 11 Ma) may even have been triggered by a plate tectonic event: the closure of the eastern Tethys gateway, the marine connection between the Mediterranean and Indian Ocean. To address this idea, we focus on the evolution of Oligocene and Miocene foreland basins in the southernmost part of Turkey, the most likely candidates to have formed this gateway. In addition, we take the geodynamic evol- ution of the Arabian-Eurasian collision into account. The Musand Elazõg ù basins, located to the north of the Bitlis- Zagros suture zone, were most likely connected during the Oligocene. The deepening of both basins is biostratigraphically dated by us to occur during the Rupelian (Early Oligocene). Deep marine conditions (between 350 and 750 m) prevailed until the Chattian (Late Oligocene), when the basins shoaled rapidly to subtidal/intertidal environment in tropical to subtropical conditions, as indicated by the macro- fossil assemblages. We conclude that the emergence of this basin during the Chattian severely restricted the marine connection between an eastern (Indian Ocean) and western (Mediterranean) marine domain. If a connection persisted it was likely located south of the Bitlis- Zagros suture zone. The Kahramanmarasbasin, located on the northern Arabian promontory south of the Bitlis- Zagros suture zone, was a foreland basin during the Middle and Late Miocene, possibly linked to the Hatay basin to the west and the Lice basin to the east. Our data indicates that this fore- land basin experienced shallow marine conditions during the Langhian, followed by a rapid dee- pening during Langhian/Serravallian and prevailing deep marine conditions (between 350 and 750 m) until the early Tortonian. We have dated the youngest sediments underneath a subduc- tion-related thrust at c. 11 Ma and suggest that this corresponds to the end of underthrusting in the Kahramanmarasregion, i.e. the end of subduction of Arabia. This age coincides in time with the onset of eastern Anatolian volcanism, uplift of the East Anatolian Accretionary Complex, and the onset of the North and East Anatolian Fault Zones accommodating westward escape tec- tonics of Anatolia. After c. 11 Ma, the foreland basin south of the Bitlis formed not (or no longer) a deep marine connection along the northern margin of Arabia between the Mediterranean Sea and the Indian Ocean. We finally conclude that a causal link between gateway closure and global climate change to a cooler mode, recorded in the Mi3b event (d18O increase) dated at 13.82 Ma, cannot be supported.
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Leuciscinae is a subfamily belonging to the Cyprinidae fish family that is widely distributed in Circum-Mediterranean region. Many efforts have been carried out to deciphering the evolutionary history of this group. Thus, different biogeographical scenarios have tried to explain the colonization of Europe and Mediterranean area by cyprinids, such as the "north dispersal" or the "Lago Mare dispersal" models. Most recently, Pleistocene glaciations influenced the distribution of leuciscins, especially in North and Central Europe. Weighing up these biogeographical scenarios, this paper constitutes not only the first attempt at deciphering the mitochondrial and nuclear relationships of Mediterranean leuciscins but also a test of biogeographical hypotheses that could have determined the current distribution of Circum-Mediterranean leuciscins. A total of 4439 characters (mitochondrial + nuclear) from 321 individuals of 176 leuciscine species rendered a well-supported phylogeny, showing fourteen main lineages. Analyses of independent mitochondrial and nuclear markers supported the same main lineages, but basal relationships were not concordant. Moreover, some incongruence was found among independent mitochondrial and nuclear phylogenies. The monophyly of some poorly known genera such as Pseudophoxinus and Petroleuciscus was rejected. Representatives of both genera belong to different evolutionary lineages. Timing of cladogenetic events among the main leuciscine lineages was gained using mitochondrial and all genes data set. Adaptations to a predatory lifestyle or miniaturization have superimposed the morphology of some species. These species have been separated into different genera, which are not supported by a phylogenetic framework. Such is the case of the genera Pseudophoxinus and Petroleuciscus, which real taxonomy is not well known. The diversification of leuciscine lineages has been determined by intense vicariant events following the paleoclimatological and hydrogeological history of Mediterranean region. We propose different colonization models of Mediterranean region during the early Oligocene. Later vicariance events promoted Leuciscinae diversification during Oligocene and Miocene periods. Our data corroborate the presence of leuciscins in North Africa before the Messinian salinity crisis. Indeed, Messinian period appears as a stage of gradually Leuciscinae diversification. The rise of humidity at the beginning of the Pliocene promoted the colonization and posterior isolation of newly established freshwater populations. Finally, Pleistocene glaciations determined the current European distribution of some leuciscine species.
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Motivation: DnaSP is a software package for a comprehensive analysis of DNA polymorphism data. Version 5 implements a number of new features and analytical methods allowing extensive DNA polymorphism analyses on large datasets. Among other features, the newly implemented methods allow for: (i) analyses on multiple data files; (ii) haplotype phasing; (iii) analyses on insertion/deletion polymorphism data; (iv) visualizing sliding window results integrated with available genome annotations in the UCSC browser. Availability: Freely available to academic users from: http://www.ub.edu/dnasp Contact: jrozas{at}ub.edu
Article
Turkey has a rich freshwater biodiversity in terms of Cyprinid genus in respect to its geographical location. To elucidate the phylogeny of the Alburnoides genus, one of these genera, genetic data for the cytochrome b gene (1141 bp) was generated for 445 samples collected at 42 sampling sites across their geographical distribution. A total of 54 mitochondrial haplotypes identified were distrubuted among distinct twelve species that did not share haplotypes with each other. Pairwise sequence divergence among these species range from 1.37% (A. emineae and A. velioglui) and 10.99% (A. manyasensis and A. smyrnae). A new potential species in the River Dirgine that run into the Black Sea Basin was separated from the most closed known species with mean 6.3%. Network analysis and phylogenetic analysis indicated that all haplotypes were clustered into two major clades, which corresponded to twenty-three Alburnoides lineages, with moderate-high bootstrap supports and mutational steps, respectively. Application of a molecular clock to a Bayesian phylogeny indicates that Alburnoides diversified under the paleogeographic conditions such as tectonic uplift and faulting Miocene aged as well as climatic oscillation and sea-level fluctuations during late Miocene-middle Pleistocene. The genetic results of the present study indicated the inter-specific distance of cyt b gene sequences followed the ideal results for species identification and phylogeny of Turkish spirlins.
Article
Alburnus magnificus, new species, is described from the northern Orontes River drainage in the eastern Mediterranean Sea basin. It is most similar and closely-related to A. qalilus from coastal rivers in Syria south of the Orontes. Alburnus magnificus is distinguished from A. qalilus by having the anal-fin origin below or behind the vertical through the last dor-sal-fin ray, 4-5 scale rows between the lateral line and the anal-fin origin, and a flank pattern of bold black, grey or brown scales on a silvery or brown background. The two species are also distinguished by a minimum K2P distance of 1.8% in their COI sequence data.
Article
Alburnus goekhani, new species, is described from the Yeşilırmak and Kızılırmak River drainages. It belongs to the A. alburnus species group and is distinguished from other species in this group in Anatolia by having 48-56 + 2-3 scales in the lateral-line, 12-15 gill rakers, a distinct dark lateral stripe along the flank on live and preserved specimens and the anal-fin origin situated below the branched dorsal-fin ray 6-8. Alburnus goekhani is also well distinguished from other Alburnus species by its DNA barcode sequence.
Article
The generic position of Leuciscus kurui Bogutskaya, 1995 is reviewed through a comparison of morphological and molecular characters (COI). The molecular data place L. kurui in Alburnus, close to Alburnus timarensis from the Lake Van basin. Alburnus kurui (Bogutskaya) is distinguished from this species by lacking a ventral keel and possessing both a very low number of gill rakers and midlateral scales. Alburnus selcuklui, from the upper Tigris drainage, cannot be distinguished from the widespread A. sellal and is therefore treated as a synonym of this species. Alburnus kurui Mangit & Yerli, 2018 is a junior secondary homonym of A. kurui (Bogutskaya, 1995) and A. carianorum is proposed as its replacement name. Several specimens of Alburnus caeruleus and Alburnus heckeli shared the same haplotypes as some A. sellal and therefore these species cannot always be distinguished by mitochondrial molecular characters. Alburnus caeruleus and A. heckeli are treated as valid species. Other individuals of A. caeruleus have haplotypes very different from A. sellal, and A. heckeli is well distinguished from A. sellal by having more gill rakers. The Lake Van basin as a separate freshwater ecoregion and the treatment of several species of Alburnus in synonymy of A. mento are discussed.
Article
Alburnus kotschyi is re-described and a neotype is designated. It is found in a small isolated coastal stream at Arsuz at the eastern Mediterranean coast as well as in the Ceyhan and Seyhan River drainages in southern Anatolia. Alburnus adanensis, from the Seyhan River, seems not to have been found again since its first description in 1944 and might be extinct.
Article
Episodes of population growth and decline leave characteristic signatures in the distribution of nucleotide (or restriction) site differences between pairs of individuals. These signatures appear in histograms showing the relative frequencies of pairs of individuals who differ by i sites, where i = 0, 1, .... In this distribution an episode of growth generates a wave that travels to the right, traversing 1 unit of the horizontal axis in each 1/2u generations, where u is the mutation rate. The smaller the initial population, the steeper will be the leading face of the wave. The larger the increase in population size, the smaller will be the distribution's vertical intercept. The implications of continued exponential growth are indistinguishable from those of a sudden burst of population growth Bottlenecks in population size also generate waves similar to those produced by a sudden expansion, but with elevated uppertail probabilities. Reductions in population size initially generate L-shaped distributions with high probability of identity, but these converge rapidly to a new equilibrium. In equilibrium populations the theoretical curves are free of waves. However, computer simulations of such populations generate empirical distributions with many peaks and little resemblance to the theory. On the other hand, agreement is better in the transient (nonequilibrium) case, where simulated empirical distributions typically exhibit waves very similar to those predicted by theory. Thus, waves in empirical distributions may be rich in information about the history of population dynamics.
Article
Haplotype networks are an intuitive method for visualising relationships between individual genotypes at the population level. Here, we present popart , an integrated software package that provides a comprehensive implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with publication‐ready figure production. popart also provides a platform for the implementation and distribution of new network‐based methods – we describe one such new method, integer neighbour‐joining . The software is open source and freely available for all major operating systems.
Chapter
The Messinian species are the oldest permanent inhabitants of the Mediterranean while most other forms are “newcomers” of Pliocene or younger age. Criteria are suggested for the recognition of old species in the recent faunal assemblages. The species-groups of the genera Cyprideis, Diamysis, and Aphanius are the most characteristic; several other species are proposed for the recent Messinian inventory. These comprise a complex of polymorphic species-groups, characterized by high genetic and phenetic variability. A comparison is made between Paratethyan and Messinian species.
Article
Alburnus carinatus from Lakes Manyas and Ulubat), A. istanbulensis (small rivers in Turkish Thrace and Lake Sapanca), A. nicaeensis (Lake lznik) and A. derjugini (River Coruh in north-eastern Anatolia) are valid species and are rediagnosed. Alburnus sapancae (from Lake Sapanca) is a simultaneous subjective synonym of A. istanbulensis and this last name has precedence. Two new species are described: Alburnus battalgilae, from River Gediz drainage and A. attalus from River Bakir drainage (Turkey).
Article
The genetic discrimination of two species of the genus Capoeta, C. tinca (Heckel, 1843) and C. banarescui Turan et al., 2006, which is represented by many endemic species in Anatolian Turkey, has been investigated by analysing the partial 16S ribosomal DNA gene (525 bp). A total of 85 fish was sampled from two localities in the Marmara basin and 5 localities in the Black Sea basin. The amount of 16S rDNA sequence divergence separating these two taxa (mean 1.19%) is within the range observed for 16S rDNA variation between other species of freshwater fishes. The derived haplotypes (h: 28) were strictly local and were not shared between species or populations within species. Three types of phylogenetic tree (Bayesian, MP and ML) clearly showed C. banarescui and C. tinca as distinct species separated with significant bootstrap values (BI:94, MP:88, ML:81), confirming previous conclusions based on morphometric and meristic characters. Furthermore, four novel SNPs were identified, allowing discrimination between two species. AMOVA tests revealed that populations of Capoeta in Northeastern Anatolia can be divided into two main groups: Coruh River group, including SVS, TRT and ISP populations, and Yesilirmak-Harsit group, consisting of ALC and HRS populations. These results indicate the effectiveness of mitochondrial 16S rDNA gene sequences for both species identification and the phylogenetic analysis of Capoeta species.
Article
The historic biogeography of the aquatic fauna of the Levant is reconstructed upon evidence of the gastropod groups with a well-established taxonomy and a rich fossil record. Faunal origins include ancient northern elements coming from an Anatolian–Iberian faunal province that, in the early Miocene, bypassed mainland Italy. This scenario is more plausible than the current ‘Lago Mare’ biogeographical theory. Palaeotropical elements represent either an Oriental or an African source; in either case these elements could have first reached Anatolia, from where they eventually spread southwards into the Levant, perhaps broadly coinciding in time with the invasion of the northern elements. Within the Levant, the faunas of the Euphrates, Orontes, and Jordan formed at first one common pool, but by 2 Mya the fauna of the Jordan had diverged from that of the Orontes; later, the Orontes fauna diverged from that of the Euphrates. By 1.4 Mya the fauna of the Levant consisted of both ancient survivors and new species. Some 780 000 years ago there was an exceptionally diversified fauna with many new, northern elements. Many of these elements did not survive to recent times. The fossil record suggests that the fauna of the Jordan Valley was separate from that of the Orontes throughout the Pliocene–Pleistocene. Taxa common today to the Jordan Valley and coastal sites may reflect an ancient system of rivers that drained westwards to the Mediterranean Sea, across the Jordan Valley of today. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 92, 625–639.
Article
A revised quantitative kinematic model has been determined for the Dead Sea Fault Zone (DSFZ) and the left-lateral fault zones in SE Turkey. The relative motions of the African and Arabian plates across the DSFZ are represented by relative rotation about 31.1°N 26.7°E at 0.40±0.02° Ma−1. The northern DSFZ, in Syria and southern Turkey, is interpreted for the first time as a series of transpressional stepovers, along which the left-lateral slip rate is substantially less than the rate of relative plate motion, because this slip is oblique to the plate motion. The slip rate on the East Anatolian Fault Zone (EAFZ) is estimated as ∼8 mm a−1. Restoring its observed slip thus requires its age to be ∼4 Ma. The previous phase of deformation, which involved slip on the Malatya–Ovacık Fault Zone (MOFZ) before the EAFZ came into being, is thus dated to ∼7–4 Ma, suggesting initiation of the North Anatolian Fault Zone (NAFZ) at ∼7 Ma, not ∼5 Ma as previously thought. The total left-lateral slip on the northern DSFZ in southernmost Turkey is estimated as at least ∼65 km, partitioned with ∼45 km on the Amanos Fault, ∼10 km on the East Hatay Fault, and a further ∼10 km on the Kırkpınar Fault farther east. Much of this slip is inferred to have occurred during the Miocene, before the modern geometry of this plate boundary zone developed. When it first formed, the AF–AR plate boundary was relatively complex—it initially reactivated preexisting structures in the Palmyra foldbelt in Syria and in the Gaziantep region of southern Turkey, which were significantly misaligned relative to the plate motion, requiring major components of shortening as well as left-lateral slip. The transition, from this initial rather diffuse geometry to the present localised geometry of the DSFZ across western Syria, occurred within the Miocene. The predicted rate of relative motion between the stable interiors of the Turkish and African plates in the vicinity of their common boundary onshore of İskenderun Gulf in southern Turkey is estimated as westward at ∼9 mm a−1. However, this “promontory” of the African plate is itself moving westward relative to the stable interior of this plate at ∼7–8 mm a−1. The rate of localised left-lateral slip on the onshore part of this boundary, the NE-trending Yakapınar–Göksun Fault, is thus estimated as only ∼2 mm a−1. This locality can also be regarded as within the distributed boundary zone between the Turkish and Arabian plates. The estimated relative motion between these plates is at ∼8.7 mm a−1 towards the SSW, partitioned between localised left-lateral slip at ∼2 mm a−1 on the Yakapınar–Göksun Fault, and at least ∼1 mm a−1 on the Amanos Fault, and ∼2.5 mm a−1 on East Hatay Fault, with at most distributed left-lateral simple shear at ∼3.2 mm a−1 across the Amanos Mountains in between. However, the combined slip on left-lateral faults east of the Amanos Mountains may be as high as ∼6 mm a−1, with slip at ∼1.7 mm a−1 on the Amanos Fault and at ∼4.3 mm a−1 on the East Hatay Fault and any active faults farther east. This requires no more than ∼0.7 mm a−1 of distributed simple shear across the Amanos Mountains, raising the possibility that this component of deformation may in fact be zero, this small nonzero estimate possibly indicating a closure error arising from minor errors in predicted values of other relative motion vectors. It is proposed that this boundary between the Turkish and African plates first developed at the same time as the MOFZ and NAFZ, but its original geometry involving left-lateral slip on the Karataş–Osmaniye Fault has since become locked by the presence of relatively strong ophiolitic crust within this fault zone. This quantitative kinematic model demonstrates, for the first time, how it is possible for the left-lateral faulting accommodating the NNW–SSE relative motion between the Arabian and African plates in NW Syria to “dovetail” into the left-lateral faulting accommodating the WSW–ENE relative motion between the Turkish and Arabian plates in SE Turkey.
Article
The development of DNA-based genetic markers has had a revolutionary impact on animal genetics. With DNA markers, it is theoretically possible to observe and exploit genetic variation in the entire genome. Popular genetic markers in the aquaculture community include allozymes, mitochondrial DNA, RFLP, RAPD, AFLP, microsatellite, SNP, and EST markers. The application of DNA markers has allowed rapid progress in aquaculture investigations of genetic variability and inbreeding, parentage assignments, species and strain identification, and the construction of high-resolution genetic linkage maps for aquaculture species. Well-designed studies using these genetic markers will undoubtedly accelerate identification of genes involved in quantitative trait loci (QTL) for marker-assisted selection. In this review, the principles, potential power, requirements, advantages, and disadvantages of the various marker types are discussed, along with their applications in a variety of aquaculture studies. Included are discussions on how to efficiently exploit research progress made from the Human Genome Project and from other model species such as zebrafish for the benefit of aquaculture genomics and aquaculture genetics research.
Article
During a stratigraphic survey of an Early Miocene sedimentary sequence outcropping in SE Slovenia an unusual enrichment of the calcareous nannoplankton assemblage with pentaliths – pentagonal nannoliths consisting of five crystal units and showing radial symmetry – was detected. Pentaliths were only abundant in a short interval, which was sampled in detail. The lithological composition of this interval was indistinguishable from that of the underlying and the overlying strata. The composition of nannoplankton assemblages and distribution patterns of different taxa were studied. Mineral composition, total calcite content and δ13C values of chosen sediment samples were analysed as well. The pentalith-enriched strata were deposited in the lower Early Miocene, corresponding to the Egerian stage of the Central Paratethys and the Aquitanian of the Mediterranean, in the Slovenian Corridor — a seaway linking the Central Paratethys and the Mediterranean. The presence of rare specimens of Discoaster druggii and Helicosphaera carteri allows stratigraphic correlation with the transition of NN1 — Triquetrorhabdulus carinatus Zone and NN2 — Discoaster druggii Zone of Martini [Martini, E., 1971. Standard Tertiary and Quarternary calcareous nannoplankton zonation. In: Farinacci, A. (Ed.), Proceedings of the II Planctonic Conference, Roma, 1970, Ed. Technoscienza, pp. 739–785]. Pentaliths belong to two species: Braarudosphaera bigelowii and Micrantholithus vesper. Both species display a wide range of morphological variation and most likely represent a group of sibling species. The pattern of distribution of both species displays obvious similarities throughout most of the studied interval. In the upper part of the studied interval B. bigelowii reaches maximum abundance, while M. vesper disappears. Since the ability of B. bigelowii to thrive in hyposaline water is well known, it appears that M. vesper tolerates reduced water salinity as well, but to a lesser extent than B. bigelowii. No significant paleoclimatic and paleogeographical changes are known in this particular region during the Early Miocene, however, the onset of far reaching extensional tectonic processes took place during this time. The enrichment of nannoplankton assemblage with pentaliths may represent a reflection of a short-lived episode of hyposaline conditions. Enhanced influx of freshwater and terrigenous material is indicated by a drop in 13C values, a rise in nannoplankton productivity and the presence of sand in some samples from the pentalith-enriched strata. The most likely causes of this episode are regional tectonic changes, associated with the onset of intensive tectonic activity in the western part of the Central Paratethys.
Article
We report four new Ar/Ar dates and 18 new geochemical analyses of Pleistocene basalts from the Karasu Valley of southern Turkey. These rocks have become offset left-laterally by slip on the N20{degrees}E-striking Amanos Fault. The geochemical analyses help to correlate some of the less-obvious offset fragments of basalt flows, and thus to measure amounts of slip; the dates enable slip rates to be calculated. On the basis of four individual slip-rate determinations, obtained in this manner, we estimate a weighted mean slip rate for this fault of 2.89{+/-}0.05mm/a ({+/-}2{sigma}). We have also obtained a slip rate of 2.68{+/-}0.54mm/a ({+/-}2{sigma}) for the subparallel East Hatay Fault farther east. Summing these values gives 5.57{+/-}0.54mm/a ({+/-}2{sigma}) as the overall left-lateral slip rate across the Dead Sea fault zone (DSFZ) in the Karasu Valley. These slip-rate estimates and other evidence from farther south on the DSFZ are consistent with a preferred Euler vector for the relative rotation of the Arabian and African plates of 0.434{+/-}0.012{degrees} Ma-1 about 31.1{degrees}N, 26.7{degrees}E. The Amanos Fault is misaligned to the tangential direction to this pole by 52{degrees} in the transpressive sense. Its geometry thus requires significant fault-normal distributed crustal shortening, taken up by crustal thickening and folding, in the adjacent Amanos Mountains. The vertical component of slip on the Amanos Fault is estimated as c. 0.15mm/a. This minor component contributes to the uplift of the Amanos Mountains, which reaches rates of c. 0.2-0.4mm/a. These slip rate estimates are considered representative of time since. 3.73{+/-}0.05Ma, when the modern geometry of strike-slip faulting developed in this region; an estimated 11km of slip on the Amanos Fault and c. 10km of slip on the East Hatay Fault have occurred since then. It is inferred that both these faults came into being, and the associated deformation in the Amanos Mountains began, at that time. Prior to that, the northern part of the Africa-Arabia plate boundary was located further east.
Article
Some simple formulae were obtained which enable us to estimate evolutionary distances in terms of the number of nucleotide substitutions (and, also, the evolutionary rates when the divergence times are known). In comparing a pair of nucleotide sequences, we distinguish two types of differences; if homologous sites are occupied by different nucleotide bases but both are purines or both pyrimidines, the difference is called type I (or "transition" type), while, if one of the two is a purine and the other is a pyrimidine, the difference is called type II (or "transversion" type). Letting P and Q be respectively the fractions of nucleotide sites showing type I and type II differences between two sequences compared, then the evolutionary distance per site is K = -(1/2) ln [(1-2P-Q) square root of 1-2Q]. The evolutionary rate per year is then given by k = K/(2T), where T is the time since the divergence of the two sequences. If only the third codon positions are compared, the synonymous component of the evolutionary base substitutions per site is estimated by K'S = -(1/2) ln (1-2P-Q). Also, formulae for standard errors were obtained. Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.