Taking advantage of reference-guided assembly in a slowly-evolving lineage: Application to Testudo graeca.

Background: Obtaining de novo chromosome-level genome assemblies greatly enhances conservation and evolutionary biology studies. For many research teams, long-read sequencing technologies (that produce highly contiguous assemblies) remain unaffordable or unpractical. For the groups that display high synteny conservation, these limitations can be overcome by a reference-guided assembly using a close relative genome.

Ten simple rules for a mom-friendly Academia.

Women (and all gender-discriminated people) are underrepresented in science, especially in leadership positions and higher stages of the scientific career. One of the main causes of career abandonment by women is maternity, with many women leaving Academia after having their first child because of the career penalties associated with motherhood. Thus, more actions to help scientific moms to balance family and academic work are urgently needed to increase representation of women and other gender discriminated people in Academia.

Predation impact on threatened spur-thighed tortoises by golden eagles when main prey is scarce.

A reduction in adult survival in long-living species may compromise population growth rates. The spur-thighed tortoise (Testudo graeca) is a long-lived reptile that is threatened by habitat loss and fragmentation. Golden eagles (Aquila chrysaetos), whose breeding habitats overlap that of tortoises, may predate them by dropping them onto rocks and breaking their carapaces.

Discordant phylogeographic patterns between the tortoise tick Hyalomma aegyptium and their Testudo graeca hosts.

Tortoise ticks, Hyalomma aegyptium, are considered so strongly associated with their hosts that they are even used as indirect indicators for them. In such a case, a robust pattern of congruence between host and parasite could be expected, with phylogeographic breaks within the host being reflected in their parasites. We sequenced two mitochondrial partial gene regions (12S rRNA and Cytochrome Oxidase 1) from ticks across northern Africa and Anatolia, and compared patterns of variation with those identified in its main host, Testudo graeca.

Differences in Reproductive Success in Young and Old Females of a Long-Lived Species.

Long-lived species are particularly interesting for investigation of trade-offs that shape reproductive allocation and the effective contribution to the next generations. Life history theory predicts that these species will buffer environmental stochasticity via changes in the reproductive investment, while maintaining high adult survival rates. The spur-thighed tortoise was selected as a case study in order to investigate the relationship between the linked maternal characteristics (size and age) and related traits in their hatchlings.

Ancient mitogenomics elucidates diversity of extinct West Indian tortoises.

We present 10 nearly complete mitochondrial genomes of the extinct tortoise Chelonoidis alburyorum from the Bahamas. While our samples represent morphologically distinct populations from six islands, their genetic divergences were shallow and resembled those among Galápagos tortoises. Our molecular clock estimates revealed that divergence among Bahamian tortoises began ~ 1.

Biotic interactions matter in phylogeography research: Integrative analysis of demographic, genetic and distribution data to account for them.

It is well established that biotic-interspecific interactions, such as competition, mutualism, parasitism or predation, modulate species dynamics in demographic and evolutionary terms. It is also acknowledged that biotic interactions can even have major effects on local population dynamics and scale-up to determine wider species' ranges (Wisz et al., 2013).

Sperm storage reduces the strength of the mate-finding Allee effect.

Mate searching is a key component of sexual reproduction that can have important implications for population viability, especially for the mate-finding Allee effect. Interannual sperm storage by females may be an adaptation that potentially attenuates mate limitation, but the demographic consequences of this functional trait have not been studied. Our goal is to assess the effect of female sperm storage durability on the strength of the mate-finding Allee effect and the viability of populations subject to low population density and habitat alteration.

Impact of habitat loss on the diversity and structure of ecological networks between oxyurid nematodes and spur-thighed tortoises ( L.).

Habitat loss and fragmentation are recognized as affecting the nature of biotic interactions, although we still know little about such changes for reptilian herbivores and their hindgut nematodes, in which endosymbiont interactions could range from mutualistic to commensal and parasitic. We investigated the potential cost and benefit of endosymbiont interactions between the spur-thighed tortoise ( L.) and adult oxyurid nematodes (Pharyngodonidae order Oxyurida) in scrublands of southern Spain.

Population density of the spur-thighed tortoise Testudo graeca declines after fire in north-western Africa.

Fire is a key ecological process in several biomes worldwide. Over recent decades, human activities (e.g.

Complex hybridization patterns in European pond turtles (Emys orbicularis) in the Pyrenean Region.

Hybrid zones are natural laboratories allowing insights in genetic processes like lineage diversification, speciation and introgression. Using large sampling, 15 microsatellite loci and a mitochondrial marker, we examined the Pyrenean contact zone of three pond turtle taxa (Emys orbicularis orbicularis, E. o.

Extra-Mediterranean glacial refuges in barred and common grass snakes (Natrix helvetica, N. natrix).

Extra-Mediterranean glacial refugia of thermophilic biota, in particular in northern latitudes, are controversial. In the present study we provide genetic evidence for extra-Mediterranean refugia in two species of grass snake. The refuge of a widely distributed western European lineage of the barred grass snake (Natrix helvetica) was most likely located in southern France, outside the classical refuges in the southern European peninsulas.

Human-mediated secondary contact of two tortoise lineages results in sex-biased introgression.

Human-mediated secondary contact of recently diverged taxa offers valuable opportunities for studying the evolutionary mechanisms involved in the establishment and maintenance of genetic boundaries between taxa. We used mitochondrial and microsatellite markers to examine a recently introduced population of the spur-thighed tortoise (Testudo graeca) of mixed origin in the Doñana National Park (SW Spain). The earliest records of tortoises in Doñana trace back to the 18th century, but several population reinforcements in the 20th century with animals from Morocco are well-documented.

Low tortoise abundances in pine forest plantations in forest-shrubland transition areas.

In the transition between Mediterranean forest and the arid subtropical shrublands of the southeastern Iberian Peninsula, humans have transformed habitat since ancient times. Understanding the role of the original mosaic landscapes in wildlife species and the effects of the current changes as pine forest plantations, performed even outside the forest ecological boundaries, are important conservation issues. We studied variation in the density of the endangered spur-thighed tortoise (Testudo graeca) in three areas that include the four most common land types within the species' range (pine forests, natural shrubs, dryland crop fields, and abandoned crop fields).

Genetic Signatures of Demographic Changes in an Avian Top Predator during the Last Century: Bottlenecks and Expansions of the Eurasian Eagle Owl in the Iberian Peninsula.

The study of the demographic history of species can help to understand the negative impact of recent population declines in organisms of conservation concern. Here, we use neutral molecular markers to explore the genetic consequences of the recent population decline and posterior recovery of the Eurasian eagle owl (Bubo bubo) in the Iberian Peninsula. During the last century, the species was the object of extermination programs, suffering direct persecution by hunters until the 70's.

Surfing in tortoises? Empirical signs of genetic structuring owing to range expansion.

Much of our current knowledge about the genetic dynamics in range expansions originates from models, simulations and microcosm experiments that need to be corroborated by field data. Here, we report a neutral genetic pattern that matches the predictions of the genetic surfing theory. Genetic surfing occurs when repeated founding events and genetic drift act on the wave of advance of an expanding population, promoting strong spatial structure.

Differences in helminth infections between captive and wild spur-thighed tortoises Testudo graeca in southern Spain: a potential risk of reintroductions of this species.

Although the spur-thighed tortoise, Testudo graeca, is one of the most widely distributed species of tortoises, its natural populations are threatened through its whole range. Particularly at south-eastern Spain, the species is mainly threatened by habitat destruction and over-collection, given that this chelonian has been traditionally considered an appreciate pet. As south-eastern Spanish wildlife recovery centers shelter hundreds of captive animals mainly coming from illegal trade or captive-bred, there is a strong debate about what to do with these animals: maintaining them in captivity all along their lives or reintroducing them to wildlife.