Nikos Poulakakis

• Professor
• Professor at University of Crete

Abstract: Crocidura zimmermanni is an insectivore mammal of the family Soricidae and the sole endemic mammal of Greece, exclusively found in the uplands of Crete. It is listed as endangered (EN-IUCN), mainly due to climate change and the human-aided introduction of C. gueldenstaedtii in historical t imes. The challenging capturing, high mortality...

Shrews are abundant in terrestrial ecosystems, yet they remain one of the most elusive mammal families of Europe. From the smallest mammal to the most speciose mammalian genus to an Endangered insular endemic species surviving since the Pleistocene, Greece hosts unique shrew communities due to its geographical heterogeneity and complex geological h...

The distribution of the neutral component of genetic diversity is the interplay of historical and ongoing processes resulting in the species-specific genetic structure of populations, which can, however, be disrupted by interspecific hybridisation and introgression. In this study, we focused on two species of water frogs, Pelophylax epeiroticus and...

A common problem when analyzing ancient DNA (aDNA) data is to identify the species which corresponds to the recovered aDNA sequence(s). The standard approach is to deploy sequence similarity based tools, such as BLAST. However, as aDNA reads may frequently stem from unsampled taxa due to extinction, it is likely that there is no exact match in any...

Land snails and the Aegean Archipelago offer an intriguing combination for studying biodiversity, biogeography and ecology. A region with high environmental and temporal heterogeneity and a tri-continental biotic influence and a group of organisms with low active dispersal abilities, high endemism, as well as the particularity to leave shells as tr...

A common problem when analyzing ancient DNA (aDNA) data is to identify the species which corresponds to the recovered aDNA sequence(s). The standard approach is to deploy sequence similarity based tools such as BLAST. However, as aDNA reads may frequently either stem from unsampled taxa due to extinction, it is likely that there is no exact match i...

The lacertid wall lizards of the genus Podarcis (Wagler, 1830) originate from Western Europe and are divided into 24-25 species (Speybroeck et al., 2020). Despite the abundance of phylogenetic studies referring to the genus, the relationships among certain species, as well as the taxonomic status of some genealogical lineages, remain unclear due to...

We present a genome assembly from an individual male Podarcis cretensis (the Cretan wall lizard; Chordata; Lepidosauria; Squamata; Lacertidae). The genome sequence is 1,507.6 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and...

After the domestication of goats around 10,000 years before the present (BP), humans transported goats far beyond the range of their wild ancestor, the bezoar goat. This brought domestic goats into contact with many wild goat species such as ibex and markhor, enabling introgression between domestic and wild goats. To investigate this, while sheddin...

The Cretan Shrew Crocidura zimmermanni (Wettstein 1953) is the only recognized endemic of Greece and one of the last Pleistocene island mammals of the Mediterranean that survive today. The species is considered endangered (EN) due to its small and fragmented populations. Limited knowledge of the ecology of the species exists and even the morphologi...

The genus Pelophylax (water frogs) includes relatively common, widely distributed, and even invasive species, but also endemic taxa with small ranges and limited knowledge concerning their ecology and evolution. Among poorly studied species belong endemics of the southwestern Balkans, namely Pelophylax shqipericus, P. epeiroticus and P. kurtmueller...

Illegal Wildlife Trade (IWT) is a cause for global concern as pressure stemming from IWT threatens wild species and can even lead to extinction. Galapagos giant tortoises (Chelonoidis sp.) are a group of threatened species protected under CITES, which forbids their import–export for international trade; however, IWT of this group persists. In this...

Galapagos giant tortoises are endemic to the Galapagos Archipelago, where they are found in isolated populations. While these populations are widely considered distinguishable in morphology, behavior, and genetics, the recent divergence of these taxa has made their status as species controversial. Here, we apply multispecies coalescent methods for...

This is a pre-print. Currently, the paper is under-review. You may download it freely from here: 10.2139/ssrn.4578618

The genus Anatololacerta is distributed in the eastern Mediterranean region including Asia Minor and some east Aegean islands. Recent phylogenetic studies suggested that this genus displayed cryptic diversity and was divided into five species: A. anatolica, A. pelasgiana, A. ibrahimi, A. finikensis and A. danfordi. The ecological niche differentiat...

Urban habitats receive an increasing number of species due to anthropogenic activities, mainly transportations. Here, we report a new addition to the herpetofauna of Athens (Greece): a small population of the Pelasgian wall lizard (Anatololacerta pelasgiana) was found in a suburb of the Athenian metropolitan area. The species normally occurs in so...

We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of complex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 present-day published genomes, we found that...

Non-volant micro mammals are an understudied group of mammals in Greece, although they are integral parts of every terrestrial ecosystem. Our study aims to investigate the distribution of the Greek micromammals through Species Distribution Models (SDMs). SDMs have gained popularity amongst ecologists due to their usefulness, accessibility and the m...

High-throughput sequencing has enabled the comprehensive genetic exploration of biological diversity, especially by using natural history collections to study hard-to-find, threatened or even extinct-in-the-wild taxa. Mollusk shells are under-exploited as a source for DNA-based approaches, despite their apparent advantages in the field of conservat...

Understanding intra-island patterns of evolutionary divergence, including cases of cryptic diversity, is a crucial step towards deciphering speciation processes. Cyprus is an oceanic island isolated for at least 5.3 Mya from surrounding continental regions, while it remains unclear whether it was ever connected to the mainland, even during the Mess...

The status of the Fernandina Island Galapagos giant tortoise (Chelonoidis phantasticus) has been a mystery, with the species known from a single specimen collected in 1906. The discovery in 2019 of a female tortoise living on the island provided the opportunity to determine if the species lives on. By sequencing the genomes of both individuals and...

The genus Phlebotomus (Diptera: Psychodidae: Phlebotominae) comprises a group of small winged insect species of medical importance. To date, ten species of Phlebotomus are known to be present in Greece; yet their evolutionary history is poorly studied due to the lack of comprehensive phylogenetic and phylogeographic studies. Herein, we aim to clari...

The smooth snake Coronella austriaca (Laurenti, 1768) is distributed across the western Palearctic throughout north‐central, southern Europe and western Asia. So far, only few phylogenetic studies, based on mitochondrial DNA, have been carried out on this species focusing mainly on the Iberian Peninsula and northern Europe, leaving unstudied some o...

The Galapagos Archipelago is recognized as a natural laboratory for studying evolutionary processes. San Cristóbal was one of the first islands colonized by tortoises, which radiated from there across the archipelago to inhabit 10 islands. Here, we sequenced the mitochondrial control region from six historical giant tortoises from San Cristóbal (fi...

Situated at the junction of three continents, Europe, Asia and Africa, the Eastern Mediterranean is an ideal region to study the effects of palaeogeography, ecology and long human presence on animal evolution. Laudakia stellio (Squamata: Agamidae) is found across this region and offers an excellent opportunity for such studies. The high morphologic...

The genus Origanum is a well-known culinary, aromatic and medicinal taxon of the Lamiaceae family. Despite the notable progress that has been made in Lamiaceae phylogenetics and in the Nepetoideae subfamily, the genus remains insufficiently investigated concerning its interspecies evolutionary relationships. The present study provides initial insig...

The Cypriot pygmy hippopotamus is an extinct Mediterranean species that inhabited the island of Cyprus during the Late Pleistocene. This iconic species last appears at the archaeological site of Akrotiri Aetokremnos, dated to ~12 500 cal. BP. Taxonomically, the Cypriot pygmy hippopotamus has been assigned to Hippopotamus minor, which, based on morp...

The Cypriot pygmy hippopotamus is an extinct Mediterranean species that inhabited the island of Cyprus during the Late Pleistocene. This iconic species last appears at the archaeological site of Akrotiri Aetokremnos, dated to ~12 500 cal. BP. Taxonomically, the Cypriot pygmy hippopotamus has been assigned to Hippopotamus minor, which, based on morp...

The Mediterranean Basin has experienced extensive change in geology and climate over the past six million years. Yet, the relative importance of key geological events for the distribution and genetic structure of the Mediterranean fauna remains poorly understood. Here, we use population genomic and phylogenomic analyses to establish the evolutionar...

The Peloponnese wall lizard, Podarcis peloponnesiacus, is endemic to the Peloponnese. Although the phylogeny and species diversity of the Balkan species of Podarcis have been extensively studied, the intraspecific relationships of P. peloponnesiacus are not yet well defined. The aim of this study was to investigate the intraspecific diversity in th...

The Mediterranean Basin has experienced extensive change in geology and climate over the past six million years. Yet, the relative importance of key geological events for the distribution and genetic structure of the Mediterranean fauna remains poorly understood. Here, we use population genomic and phylogenomic analyses to establish the evolutionar...

We still have little knowledge concerning the phylogeography of amphibians and reptiles from the Balkan Peninsula compared with the other two Mediterranean peninsulas. This raises concerns for endemic taxa from these peninsulas, because it might interfere with further conservation efforts. Here we focus on the endemic Greek stream frog (Rana graeca...

Wall lizards of the genus Podarcis (Sauria, Lacertidae) are the predominant reptile group in southern Europe, including 24 recognized species. Mitochondrial DNA data have shown that, with the exception of P. muralis, the Podarcis species distributed in the Balkan peninsula form a species group that is further sub-divided into two subgroups: the one...

Genetic diversity is not always congruent with phenotypic heterogeneity, resulting in cryptic species complexes which cause a great struggle for scientists trying to define ‘species’ and describe relationships among taxa. Anatololacerta is a lizard genus distributed in southern and western Anatolia and some neighboring Aegean islands. Three morphos...

The area of the south‐western Balkans hosts a remarkably high species richness and has been considered a biodiversity hotspot. The significance of the Balkan Peninsula as a biodiversity refugium during the Quaternary climatic fluctuations has been repeatedly pointed out in literature, yet the area remains quite understudied in terms of phylogeograp...

Abstract Molecular species identification plays a crucial role in archaeology and palaeontology, especially when diagnostic morphological characters are unavailable. Molecular markers have been used in forensic science to trace the geographic origin of wildlife products, such as ivory. So far, only a few studies have applied genetic methods to both...

Galapagos giant tortoises (Chelonoidis spp.) are a group of large, long‐lived reptiles that includes 14 species, 11 of which are extant and threatened by human activities and introductions of non‐native species. Here, we evaluated the phylogenetic relationships of all extant and two extinct species (Chelonoidis abingdonii from the island of Pinta a...

The Aegean archipelago, as an 'evolutionary laboratory of nature', is an ideal model for research in phylogeography. In this area, the darkling beetles of the genus Dendarus (distributed from Morocco to the Caucasus) exhibit a high level of diversity with 36 species, 27 of which are island endemics. However, their taxonomy is complex and unstable,...

The Aegean archipelago, as an ‘evolutionary laboratory of nature’, is an ideal model for research in phylogeography. In this area, the darkling beetles of the genus Dendarus (distributed from Morocco to the Caucasus) exhibit a high level of diversity with 36 species, 27 of which are island endemics. However, their taxonomy is complex and unstable,...

The genus Pelophylax has been considered a model organism for understanding hybridization. Despite being the most diverse within the Western Palearctic group of Pelophylax , the ridibundus / bedriagae lineage that includes six species, remains largely understudied, revealing many knowledge gaps in regards to their evolution and conservation. Using...

Abstract Herein we present the recently founded Hellenic Evolutionary Society (HEVOS) that has been recently instituted to promote evolution and scientific thinking among the Greek-speaking public. HEVOS is a timely initiative, given the low levels of acceptance of evolution by Greek society and the almost complete lack of evolution teaching in pri...

Background: The Kastellorizo island group (in the Dodecanese, Greece) is situated in the southeast corner of the Aegean Archipelago. It consists of twenty islets, of which the three largest (Kastellorizo, Ro and Strongyli) and seven smaller ones belong to Greece. Knowledge of the malacofauna on the islands is relatively poor. Only eight species we...

Small mammals are key elements of terrestrial ecosystems, yet in south-eastern Europe many questions about their taxonomy and distribution remain unanswered. This is particularly true for the small mammal fauna of Greece. We investigated the distribution of small mammals in the district of Evros (NE Greece) through Tyto alba pellet analysis and liv...

Abstract: The genus Algyroides (Lacertidae) is distributed in southern Europe and consists of four species. Two of them (Algyroides nigropunctatus and A. moreoticus) occur in the Balkan Peninsula. Two main location-specific color phenotypes are recognized for A. nigropunctatus that currently correspond to different subspecies, whereas A. moreoticus...

Introduction/Aim: The small mammals of Greece are comprised of 43 species which belong in the orders of Insectivores and Rodents, and they are a vital component of terrestrial ecosystems, but due to the cryptic ecology these species are poorly studied. Our aim is the study of distribution of the small mammals of Greece as well as the correlation of...

The evolutionary history of taxa with limited overseas dispersal abilities is considered to be majorly influenced by vicariant events constituting them as model organisms for the interpretation of evolutionary processes. An excellent candidate are the wall lizards of the genus Podarcis exhibiting an impressive level of genetic and morphological div...

The major histocompatibility complex (MHC) has long served as a model for the evolution of adaptive genetic diversity in wild populations. Pathogen-mediated selection is thought to be a main driver of MHC diversity, but it remains elusive to what degree selection shapes MHC diversity in complex biogeographical scenarios where other evolutionary pro...

Giant tortoises are among the longest-lived vertebrate animals and, as such, provide an excellent model to study traits like longevity and age-related diseases. However, genomic and molecular evolutionary information on giant tortoises is scarce. Here, we describe a global analysis of the genomes of Lonesome George—the iconic last member of Chelono...

Introduction/Aim: The small mammals of Greece are comprised of 43 species which belong in the orders of Insectivores and Rodents, and they are a vital component of terrestrial ecosystems. In Greece there is a lack of knowledge of their distribution and taxonomy. Our aim is the study of distribution of the small mammals of Greece as well as the corr...

Keywords:digital imaging, morphometrics, taxonomy, aquatic invertebrates, Crete Purpose:The digital imaging of the aquatic invertebrates of Crete and their special traits, which are used as classification tools. The above-mentionedimaging will enrich the digital collections of the NHMC and enhance the educational applications.Methods:Several photog...

Aegean Islands host a rich herpetofauna comprising a plethora of endemic taxa. Since the early 19th century, this unique diversity attracted numerous herpetologists that described the Greek species and provided records of their distribution. Interestingly, many new records on insular ranges are still added to the literature every year. During the l...

Natural interspecific hybridization might be more important for the evolutionary history and speciation of animals than previously thought, considering several demographic and life history traits as well as habitat disturbance as factors that promote it. In this aspect, cetaceans comprise an interesting case in which the occurrence of sympatric spe...

The Balkan Peninsula constitutes a biodiversity hotspot with high levels of species richness and endemism. The complex geological history of the Balkans in conjunction with the climate evolution are hypothesized as the main drivers generating this biodiversity. We investigated the phylogeography, historical demography, and population structure of c...

In this study we aimed to clarify the identity of a wall lizard population that deviates phenotypically from the other Podarcis lizards that occur in the broader area (Athens, Greece). To this end we used molecular techniques. Most surprisingly, we identified the focal population as Podarcis vaucheri, a species far away from its natural range. Mole...

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

Background Phlebotomine sand flies (Diptera: Psychodidae) are vectors of Leishmania spp., protozoan parasites responsible for a group of neglected diseases called leishmaniases. Two sand fly genera, Phlebotomus and Sergentomyia, contain species that are present in the Mediterranean islands of Crete and Cyprus where the visceral (VL), cutaneous (CL)...

Species are being lost at an unprecedented rate due to human-driven environmental changes. The cases in which species declared extinct can be revived are rare. However, here we report that a remote volcano in the Galápagos Islands hosts many giant tortoises with high ancestry from a species previously declared as extinct: Chelonoidis elephantopus o...

Hgh-throughput DNA sequencing allows efficient discovery of thousands of single nucleotide polymorphisms (SNPs) in non-model species. Population genetic theory predicts that this large number of independent markers should provide detailed insights into population structure, even when only a few individuals are sampled. Still, sampling design can ha...

High-throughput DNA sequencing allows efficient discovery of thousands of single nucleotide polymorphisms (SNPs) in non-model species. Population genetic theory predicts that this large number of independent markers should provide detailed insights into population structure, even when only a few individuals are sampled. Still, sampling design can h...

Species are being lost at an unprecedented rate due to human-driven environmental changes. The cases in which species declared extinct can be revived are rare. However, here we report that a remote volcano in the Galápagos Islands hosts many giant tortoises with high ancestry from a species previously declared as extinct: Chelonoidis elephantopus o...

Albinaria (Gastropoda, Clausiliidae) is a pulmonate genus distributed around the north-eastern coasts of the Mediterranean. It is the most 'speciose' genus within the family of Clausiliidae, exhibiting a high degree of morphological and genetic differentiation, and serving as a model for several ecological, systematics and evolutionary studies. Nev...