Contrasting patterns of population subdivision and historical demography in three western Mediterranean lizard species inferred from mitochondrial DNA variation

Pleistocene climatic oscillations were a major force shaping genetic variability in many taxa. We analyse the relative effects of the ice ages across a latitudinal gradient in the Western Mediterranean region, testing two main predictions: (i) species with historical distributions in northern latitudes should have experienced greater loss of suitable habitat, resulting in higher extinction of historical lineages than species distributed in southern latitudes, where the effects of the ice ages were not as drastic. This would be reflected in the observation of lower diversity and number of differentiated lineages in northern areas. (ii) a signature of demographic expansion following the climate amelioration should be obvious in northern species, whereas in the south evidence of long-term effective population size stability should be observed. We used as models three species of wall lizards (Podarcis bocagei, Podarcis carbonelli and Podarcis vaucheri) that replace each other along the study area. We investigated the patterns of mitochondrial DNA diversity and subdivision and obtained demographic parameter estimates for each species. Our results suggest that P. bocagei, the northernmost species, bears low genetic diversity, a shallow coalescent history and marks of a demographic expansion. In contrast, P. vaucheri, the species with a southernmost distribution, shows deeper coalescence events, complex geographical substructure and no evidence for population growth. The species with an intermediate distribution, P. carbonelli, shows average levels of diversity, substructure and population growth. Taken together, these results conform to our main predictions and are explained by a differential influence of the ice ages on distinct latitudes.     

Small-scale distribution of a cnidarian population in the western Mediterranean

The neritic area of the coast of Catalonia (north–westMediterranean) has a continental shelf narrower in the northernhalf and broader in the southern half. This area is crossedfrom north to south by a coastal current whose intensity decreasesto the south. Both conditions, together with other local geographicaland hydrographical features, are thought to be the key factorsin determining the distribution of planktonic cnidarian assemblages,along two main variational axes: a north-south axis and a coast-opensea axis. Aiming to find support to this hypothesis, the planktoniccnidarians collected in two seasons of the year 1983 have beenstudied. The first season (April–May) corresponds to thehighest abundance and heterogeneity, and the second (September–October),to the epoch when the cnidarian population is lower, but constant,along the coastal area. In a global principal component analysisthe factor that best explains the group distribution in thearea is the coastal character, as given by the bottom depthof the sampling station. The number of individuals is greaternear the coast (due to the dominance of a euryhaline species,Muggiaea atlantica), but the species number increases towardsthe open sea (due to the addition of more oceanic species, suchas Narcomedusae and Trachymedusae and the effect of a permanenthydrographic front at the shelf-slope boundary). The secondfactor is the latitudinal axis. The northern half of the coastis under the influence of waters favouring a greater numberof species and individuals. On the contrary, the southern halfshows a less marked influence of the north–south current,their cnidarian assemblages being more constant over time. Althoughthe global cnidarian population follows this general pattern,the most abundant and frequent species (M.atlantica and Aglaurahemistoma) show a broad distribution over all the studied areabecause they are rather insensitive to hydrographical variations.     

The demography of an increasing insular Eurasian Scops Owl (Otus scops) population in western France

Rapid population declines of many long-distance Afro-Palaearctic migratory bird species are ongoing across Europe but the demographic drivers are often poorly understood, thereby limiting the development of appropriate conservation actions. Using long-term population monitoring (39 years), capture–mark–recapture data and a matrix model, we estimated demographic parameters and the effect of climate variables on adult survival, and modelled the dynamics of an increasing population of Eurasian Scops Owls Otus scops in a landscape with agricultural abandonment in western France. The observed mean annual population growth rate was 1.055 (from 68 to 523 territorial males between 1981 and 2019). Over the study period, clutch size and hatching success were stable, but fledging success and breeding success showed slight negative trends, probably due to density-dependence. Survival varied with age, with an increase during early life and evidence for rapid senescence from 4 years old. Adult survival remained stable and was positively linked to the amount of autumn rainfall in the Sahel and to the winter North Atlantic Oscillation. Survival of younger age-classes made the largest contribution to the variance of the population growth rate, followed by clutch size, fledging success and survival of older birds. Such a long-term population increase in a landscape where intensive agriculture has decreased by 64.6% sheds some new light on the causes of the decline of European Scops Owl and other Afro-Palaearctic bird populations. We infer some of the possible causes of this large-scale decline, in particular food shortage, and discuss conservation measures that could be applicable to reverse this trend.     

Estimation of age structure in anthropological demography.

The past decade has produced considerable debate over the feasibility of paleodemographic research, with much attention focusing on the question of reliability of age estimates. We show here that in cases where age is estimated rather than known, the traditional method of assigning individuals to age classes will produce biased estimates of age structure. We demonstrate the effect of this bias both mathematically and by computer simulation, and show how a more appropriate method from the fisheries literature (the "iterated age length key") can be used to estimate age structure. Because it is often the case that ages are also estimated for extant groups, we suggest that our results are relevant to the general field of anthropological demography, and that it is time for us to improve the statistical basis for age structure estimation. We further suggest that the oft noted paucity of older individuals in skeletal collections is a simple result of the use of inappropriate methods of age estimation, and that this problem can be rectified in the future by using maximum likelihood estimates of life table or hazard functions incorporating the uncertainty of age estimates.     

濒危植物银杉的种群统计与年龄结构

通过对银杉主要群落种群的数量统计和年龄组成的分析,编绘了银杉种的特定时间生命表,存活曲线和年龄结构图,结果表明,银杉种群年龄超过２００ａ后,出现植株个体死亡高峰,种群的平均生命期望陡降,预示着种群的生理衰退。银杉种群的存活曲线介于ＤｅｅｖｅｙＩ和ＩＩ型曲线之间整个银杉种群在４０龄级以上的年龄结构基本表现为增长型,但不同的银杉群落种群的年龄结构差异很大,大部分种群都存在的幼龄个体缺乏的现象,其中花坪     

The western Mediterranean region provided the founder population of domesticated narrow-leafed lupin

Key message

This study revealed that the western Mediterranean provided the founder population for domesticated narrow-leafed lupin and that genetic diversity decreased significantly during narrow-leafed lupin domestication.

Abstract

The evolutionary history of plants during domestication profoundly shaped the genome structure and genetic diversity of today’s crops. Advances in next-generation sequencing technologies allow unprecedented opportunities to understand genome evolution in minor crops, which constitute the majority of plant domestications. A diverse set of 231 wild and domesticated narrow-leafed lupin (Lupinus angustifolius L.) accessions were subjected to genotyping-by-sequencing using diversity arrays technology. Phylogenetic, genome-wide divergence and linkage disequilibrium analyses were applied to identify the founder population of domesticated narrow-leafed lupin and the genome-wide effect of domestication on its genome. We found wild western Mediterranean population as the founder of domesticated narrow-leafed lupin. Domestication was associated with an almost threefold reduction in genome diversity in domesticated accessions compared to their wild relatives. Selective sweep analysis identified no significant footprints of selection around domestication loci. A genome-wide association study identified single nucleotide polymorphism markers associated with pod dehiscence. This new understanding of the genomic consequences of narrow-leafed lupin domestication along with molecular marker tools developed here will assist plant breeders more effectively access wild genetic diversity for crop improvement.

     

Fin whale (Balaenoptera physalus) population identity in the western Mediterranean Sea

Archival bottom‐mounted audio recorders were deployed in nine different areas of the western Mediterranean Sea, Strait of Gibraltar, and adjacent North Atlantic waters during 2006–2009 to study fin whale (Balaenoptera physalus) seasonal presence and population structure. Analysis of 29,822 recording hours revealed typical long, patterned sequences of 20 Hz notes (here called “song”), back‐beats, 135–140 Hz notes, and downsweeps. Acoustic parameters (internote interval, note duration, frequency range, center and peak frequencies) were statistically compared among songs and song notes recorded in all areas. Fin whale singers producing songs attributable to the northeastern North Atlantic subpopulation were detected crossing the Strait of Gibraltar and wintering in the southwestern Mediterranean Sea (Alboran basin), while songs attributed to the Mediterranean were detected in the northwest Mediterranean basin. These results suggest that the northeastern North Atlantic fin whale distribution extends into the southwest Mediterranean basin, and spatial and temporal overlap may exist between this subpopulation and the Mediterranean subpopulation. This new interpretation of the fin whale population structure in the western Mediterranean Sea has important ecological and conservation implications. The conventionally accepted distribution ranges of northeastern North Atlantic and Mediterranean fin whale subpopulations should be reconsidered in light of the results from this study.     

Age and growth of the dusky grouper Epinephelus marginatus (Lowe 1834) in an exploited population of the western Mediterranean Sea

The age and growth of the dusky grouper, Epinephelus marginatus , in the Balearic Islands (western Mediterranean) were studied by otolith analysis from a sample of 358 specimens ranging in total length ( L _T) from 6·6 to 105·6 cm. The specimens came from commercial artisanal and recreational spear fisheries between 1999 and 2003. Otoliths grew asymmetrically throughout the range of L _T studied, showing a clear pattern of alternating translucent and opaque bands. Marginal increment analysis of specimens up to 8 years-old indicated that a single opaque band was formed each year during spring and summer. Whole otoliths allowed ageing specimens up to 10 years old, but above that age whole otoliths yielded lower age estimates than sectioned otoliths. The maximum estimated age was 61 years, which significantly extends the estimated life span of the species from a maximum of 36 years in a previous study. The von Bertalanffy growth parameters were estimated as L _∞= 95·5 cm L _T, K = 0·087 and T _O=−1·12. The study revealed differences in mean L _T at age and age structure between the shallow- and deep-water samples which may be attributed to different fishing pressure and environmental conditions.     

Mortality and age differences in marriage.

Data from the 1971 census population were used to evaluate the effects of age differences of married partners on mortality rates. Different age groups were isolated to highlight the association between mortality and age of spouse for specific ages of married men and women. Men married to much younger or to older women exhibited a higher mortality rate than men married to women who were only a few years younger than themselves. A similar trend was observed among women married to much younger or much older men compared with those whose spouses were a few years older or of similar ages as themselves. Trends for other age groups (women aged 60-69 years, men below 40, and women below 30) did not exhibit a clear pattern. Although statistical biases within age groups may in part account for the differences in the findings, the trend which emerged from the analysis suggests that lower morbidity is associated with the most common age combinations (husbands same age or slightly older than wives). Other factors could also account for the differences (e.g., selection of healthy partners in 1st marriages, differences in lifestyles between married and single).     

The Opecoelidae (Digenea) of sparid fishes of the western Mediterranean. I. Pachycreadium Manter, 1954

Problems of the systematics of the Opecoelidae in the Mediterranean region are discussed. The genus Pachycreadium Manter, 1954 is redefined and its validity commented upon. Pachycreadium carnosum (Rud., 1819) is described from Sparus pagrus and Pagellus erythrinus off Corsica (Scandola) and compared with P. gastrocotylum (Manter, 1940) and P. lerneri Sogandares-Bernal, 1959.

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Résumé Les problèmes concernant la systématique des Opécoelidés de la région méditerranéenne sont abordés. Les auteurs redéfinissent et discutent la validité du genre Pachycreadium Manter, 1954. Pachycreadium carnosum (Rudolphi, 1819) est décrit à partlr d'exemplaires parasites de Sparus pagrus et de Pagellus erythrinus des côtes de Corse (Scandola), puis comparé à P. gastrocotylum (Manter, 1940) et à P. lerneri Sogandares-Bernal, 1959.

     

Historical colonization and demography of the Mediterranean damselfish, Chromis chromis

The desiccation of the Mediterranean Sea during the Messinian Salinity Crisis 6.0-5.3 million years ago (Ma), caused a major extinction of the marine ichthyofauna of the Mediterranean. This was followed by an abrupt replenishment of the Mediterranean from the Atlantic after the opening of the Strait of Gibraltar. In this study, we combined demographic and phylogeographic approaches using mitochondrial and nuclear DNA markers to test the alternative hypotheses of where (Atlantic or Mediterranean) and when (before or after the Messinian Salinity Crisis) speciation occurred in the Mediterranean damselfish, Chromis chromis. The closely related geminate transisthmian pair Chromis multilineata and Chromis atrilobata was used as a way of obtaining an internally calibrated molecular clock. We estimated C. chromis speciation timing both by determining the time of divergence between C. chromis and its Atlantic sister species Chromis limbata (0.93-3.26 Ma depending on the molecular marker used, e.g. 1.23-1.39 Ma for the control region), and by determining the time of coalescence for C. chromis based on mitochondrial control region sequences (0.14-0.21 Ma). The time of speciation of C. chromis was always posterior to the replenishment of the Mediterranean basin, after the Messinian Salinity Crisis. Within the Mediterranean, C. chromis population structure and demographic characteristics revealed a genetic break at the Peloponnese, Greece, with directional and eastbound gene flow between western and eastern groups. The eastern group was found to be more recent and with a faster growing population (coalescent time = 0.09-0.13 Ma, growth = 485.3) than the western group (coalescent time = 0.13-0.20 Ma, growth = 325.6). Our data thus suggested a western origin of C. chromis, most likely within the Mediterranean. Low sea water levels during the glacial periods, the hydrographic regime of the Mediterranean and dispersal restriction during the short pelagic larval phase of C. chromis (18-19 days) have probably played an important role in C. chromis historical colonization.     

A population genomics insight into the Mediterranean origins of wine yeast domestication

The domestication of the wine yeast Saccharomyces cerevisiae is thought to be contemporary with the development and expansion of viticulture along the Mediterranean basin. Until now, the unavailability of wild lineages prevented the identification of the closest wild relatives of wine yeasts. Here, we enlarge the collection of natural lineages and employ whole‐genome data of oak‐associated wild isolates to study a balanced number of anthropic and natural S. cerevisiae strains. We identified industrial variants and new geographically delimited populations, including a novel Mediterranean oak population. This population is the closest relative of the wine lineage as shown by a weak population structure and further supported by genomewide population analyses. A coalescent model considering partial isolation with asymmetrical migration, mostly from the wild group into the Wine group, and population growth, was found to be best supported by the data. Importantly, divergence time estimates between the two populations agree with historical evidence for winemaking. We show that three horizontally transmitted regions, previously described to contain genes relevant to wine fermentation, are present in the Wine group but not in the Mediterranean oak group. This represents a major discontinuity between the two populations and is likely to denote a domestication fingerprint in wine yeasts. Taken together, these results indicate that Mediterranean oaks harbour the wild genetic stock of domesticated wine yeasts.     

The American brine shrimp as an exotic invasive species in the western Mediterranean

The hypersaline environments and salterns present in the western Mediterranean region (including Italy, southern France, the Iberian Peninsula and Morocco) contain autochthonous forms of the brine shrimp Artemia, with parthenogenetic diploid and tetraploid strains coexisting with the bisexual species A. salina. Introduced populations of the American brine shrimp A. franciscana have also been recorded in these Mediterranean environments since the 1980s. Based on brine shrimp cyst samples collected in these countries from 1980 until 2002, we were able to establish the present distribution of autochthonous brine shrimps and of A. franciscana, which is shown to be an expanding invasive species. The results obtained show that A. franciscana is now the dominant Artemia species in Portuguese salterns, along the French Mediterranean coast and in Cadiz bay (Spain). Co-occurrence of autochthonous (parthenogenetic) and American brine shrimp populations was observed in Morocco (Mar Chica) and France (Aigues Mortes), whereas A. franciscana was not found in Italian cyst samples. The results suggest these exotic A. franciscana populations originate as intentional or non-intentional inoculations through aquacultural (hatchery effluents) or pet market activities, and suggest that the native species can be rapidly replaced by the exotic species. This revised version was published online in July 2006 with corrections to the Cover Date.     

Understanding population structure and historical demography in a conservation context: population genetics of an endangered fern

The construction of the world's largest hydroelectric scheme across the Yangtze River, the Three Gorges Dams (TGD), in the centre of a southern-central Chinese biodiversity hot spot, the Three Gorges Reservoir Area (TGRA), has attracted international concern and conservation action. To examine whether landscape changes to date have impacted regional flora, and to establish long-term monitoring baselines, we assessed the distribution and dynamics of an endangered and TGRA endemic fern, Adiantum reniforme var. sinense . For eight nuclear microsatellites, high levels of genetic diversity ( H _E = 0.653–0.781) and slightly elevated inbreeding ( F _IS = 0.077–0.197) were found across 13 surveyed populations. The population history of this fern is characterized by a balance of gene flow and genetic drift, where historical dispersal, inferred from coalescent ( F =  0.129) and genetic differentiation ( F _ST = 0.094 and R _ST = 0.180) approaches, is moderate, reflecting an isolation by distance relationship. Importantly, most populations exhibited mutation-drift disequilibrium, suggesting a recent population decline, which is congruent with the known demographic history of the species following dam-related activities. Based on these results, populations of A. reniforme var. sinense are expected to lose genetic diversity and increase genetic structure as dam-related activities decrease size and increase genetic isolation of remnants.     

Genetic demography of the Kuznetsk Basin population: changes in marriage assortativeness with respect to ethnicity and age in the Belovo city population with time

A genetic demographic study has been performed in the city of Belovo with the use of the data on marriages contracted there in 1970 and 1994-1999. Marriage assortativeness with respect to age has been found to be the strongest and remain unchanged during the lifetime of one generation (r = 0.730 in 1970 and r = 0.801 in 1994-1999). Monoethnic marriages were substantially more frequent than interethnic ones in the Belovo population during the period studied, although the ethnic marriage assortativeness considerably decreased (K = 0.386 in 1970 and K = 0.141 in 1994-1999). Panmixia has been observed in the Russian population of Belovo. Other Eastern Slavs (Ukrainians and Belarussians) are characterized by negative marriage assortativeness and panmixia; positive marriage assortativeness has been found in other ethnic groups.     

Changing female spacing behaviour and demography in an enclosed breeding population of Clethrionomys glareolus

The social organization of Clethrionomys glareolus Schreber was studied by live trapping in an enclosure of 0.8 ha in Central Finland between the years 1982–1986. The enclosure consisted of three habitats: abandoned field, brushwood, and moist spruce heath forest.
The population density increased from 50 voles ha⁻¹ in 1982 and 1983 to 150 ha⁻¹ in 1984 and 1985. In the summer of 1986 the population crashed to almost zero. In the summer of 1984 after winter breeding the number of breeding females grew to 22 compared with 6–7 in previous years. In 1984 the mature females changed from territorial to group behaviour.
During the high population density in 1984 and 1985 breeding stopped already in late July – early August, thus preventing any fence effect.
The present study supports the hypothesis stating that microtine social organization is an opportunistic strategy reacting phenotypically to changing environmental – especially food – conditions.