Martina Pavlek

• PhD
• PostDoc Position at Rudjer Boskovic Institute

A genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 mil...

Groundwater ecosystems are inhabited by unique assemblages of animals, often with restricted distributions and highly specialized traits. Those assemblages sustain ecosystem functioning and contribute to important ecosystem services. Knowledge of the species occurring in those habitats and the main ecological and historical drivers for their distri...

The family Dysderidae is a highly diverse group of nocturnal ground‐dwelling and active‐hunter spiders. Dysderids are mostly restricted to the Western Palearctic, and particularly rich and abundant around the Mediterranean region. Interestingly, the distribution of species richness among its 24 genera and three subfamilies is highly biased—80% of i...

5S ribosomal DNAs (rDNAs) are arranged in tandem and are often under-represented in genome assemblies. In the present study, we performed a global and in-depth analysis of the 5S rDNAs in the model insect Tribolium castaneum and its closely related species Tribolium freemani. To accomplish this goal, we used our recently published genome assemblies...

Aim Quantifying the relative contribution of environmental filtering versus limiting similarity in shaping communities is challenging because these processes often act simultaneously and their effect is scale‐dependent. Focusing on caves, island‐like natural laboratories with limited environmental variability and species diversity, we tested: (i) t...

This study presents the first molecular phylogenetic analysis of the Clinocerinae, challenging the traditionally accepted monophyly of this subfamily. DNA was extracted from fresh and museum specimens representing all biogeographical regions. Maximum likelihood (ML) and Bayesian inference (BI) phylogenetic analyses were performed based on sequences...

Climate change affects all ecosystems, but subterranean ecosystems are repeatedly neglected from political and public agendas. Cave habitats are home to unknown and endangered species, with low trait variability and intrinsic vulnerability to recover from human-induced disturbances. We studied the annual variability and cyclicity of temperatures in...

The Dinaric Karst is a global hotspot for subterranean diversity, with two distinct peaks of species richness in the northwest and southeast, and an area of a lower species richness in the central part. In this article, we present a species list and describe the ecological conditions of the Lukina jama–Trojama cave system, located in the central pa...

Understanding how species assemble into communities is a central tenet in ecology. One of the most elusive questions is the relative contribution of environmental filtering versus limiting similarity. Important advances in this area have been achieved by looking at communities through a functional lens (i.e., the traits they express), so as to deri...

Geometric regularity of spider webs has been intensively studied in orb-weaving spiders, although it is not exclusive of orb weavers. Here, we document the geometrically regular, repetitive elements in the webs of the non-orb-weaving groups Leptonetidae and Telemidae for the first time. Similar to orb weavers, we found areas with regularly spaced p...

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prere...

The subterranean ecosystem exerts strong selection pressures on the organisms that thrive in it. In response, obligate cave-dwellers have developed a series of morphological, physiological, and behavioral adaptations, such as eye reduction, appendage elongation, low metabolic rates or intermittent activity patterns, collectively referred to as trog...

In the internet era, the digital architecture that keeps us connected and informed may also amplify the spread of misinformation. This problem is gaining global attention, as evidence accumulates that misinformation may interfere with democratic processes and undermine collective responses to environmental and health crises. In an increasingly poll...

The genus Troglohyphantes Joseph, 1882 (Araneae, Linyphiidae) includes 131 species, mainly distributed across the main European mountain ranges. The Alps and the north-western Dinarides account for 66 species, most of them showing narrow or even point-like distributions. The majority of Troglohyphantes spiders dwell in subterranean habitats includi...

Caves put strong constraints on organisms living there, which results in acquisition of variety of troglomorphic traits, most obvious ones being depigmentation and degradation of visual system (Christiansen 2012). Cave habitats are considered fragmented, and the animals living there face limited connectivity between potential habitats (Barr 1967, B...

Subterranean ecosystems are among the most widespread environments on Earth, yet we still have poor knowledge of their biodiversity. To raise awareness of subterranean ecosystems, the essential services they provide, and their unique conservation challenges, 2021 and 2022 were designated International Years of Caves and Karst. As these ecosystems h...

The genus Troglohyphantes Joseph, 1881 (Araneae, Linyphiidae) includes 131 species, mainly distributed across the main European mountain ranges. The Alps and the North-western Dinarides account for 66 species, most of them showing narrow or even point-like distributions. The majority of Troglohyphantes spiders dwell in subterranean habitats includi...

Species traits are an essential currency in ecology, evolution, biogeography, and conservation biology. However, trait databases are unavailable for most organisms, especially those living in difficult-to- access habitats such as caves and other subterranean ecosystems. We compiled an expert-curated trait database for subterranean spiders in Europe...

Many ecological and evolutionary studies require to quantify the degree of adaptation of subterranean species to caves or other subterranean systems. In 1962, Kenneth A. Christiansen (1924-2017) coined the term "troglomorphism" to illustrate the process of subterranean adaptation and the suite of adaptive traits of organisms ("troglomorphic traits"...

Mass media plays an important role in the construction and circulation of risk perception associated with animals. Widely feared groups such as spiders frequently end up in the spotlight of traditional and social media. We compiled an expert-curated global database on the online newspaper coverage of human-spider encounters over the past ten years...

Brazil’s caves, home to diverse species and minerals, were stripped of protections by a recent presidential decree.

In the Internet era, the digital architecture that keeps us connected and informed may collaterally amplify the spread of misinformation and falsehood1,2. The magnitude of this problem is gaining global relevance3, as evidence accumulates that misinformation interferes with democratic processes and undermines collective responses to environmental a...

Auteurs : European Reference Genome Atlas (ERGA) Consortium 3

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics,...

The genus Stygopholcus Kratochvíl, 1932 is endemic to the Balkan Peninsula and includes only four nominal species: the epigean S. photophilus Senglet, 1971 in the south (Greece to Albania) and the ‘northern clade’ consisting of three troglophile species ranging from Croatia to Albania: S. absoloni (Kulczyński, 1914); S. skotophilus Kratochvíl, 1940...

As karst phenomena, caves represent the most secluded, but also the most fascinating natural values of the Island of Mljet. Many of them contain a diverse rare and endemic subterranean fauna; impressive cave formations (speleothems), and archaeological artifacts which bear witness to the first inhabitants of the Island of Mljet who frequented the u...

Aim To disentangle the role of evolutionary history, competition and environmental filtering in driving the niche evolution of four closely related subterranean spiders, with the overarching goal of obtaining a mechanistic description of the factors that determine species' realized distribution in simplified ecological settings. Location Dinaric k...

Satellite DNAs (satDNAs) are long arrays of tandem repeats typically located in heterochromatin and span the centromeres of eukaryotic chromosomes. Despite the wealth of knowledge about satDNAs, little is known about a fraction of short, satDNA-like arrays dispersed throughout the genome. Our survey of the Pacific oyster Crassostrea gigas sequenced...

The genus Harpactea Bristowe, 1939 (Araneae, Dysderidae) is one of the most diverse and abundant components of the Mediterranean ground-dwelling spider fauna. However, the taxonomic boundaries of the genus are unclear and its monophyly has been questioned, yet never tested, in a quantitative framework. The only taxonomic revisions in the genus trac...

Projektom Biospeleološka istraživanja i inventarizacija faune u speleološkim objektima Nacionalnog parka Sjeverni Velebit u suradnji Javne ustanove "Nacionalni park Sjeverni Velebit" i Hrvatskog biospeleološkog društva, biospeleološki je istraženo 5 speleoloških objekata: Jama pod Budinom kosicom, Jama u kuku, Sniježnica u Medvjeđoj dolini, Špilja...

One of the most striking features of obligate subterranean species is their narrow distribution ranges. These prevail not only at specific, but often also at generic level. However, some subterranean genera have continental scale and disjunct distribution , which challenges their monophyly and questions the scenarios of their origin and colonizatio...

Macroecologists seek to identify drivers of community turnover (β-diversity) through broad spatial scales. However, the influence of local habitat features in driving broad-scale β-diversity patterns remains largely untested, owing to the objective challenges of associating local-scale variables to continental-framed datasets. We examined the relat...

Background Spiders (Arachnida: Araneae) are widespread in subterranean ecosystems worldwide and represent an important component of subterranean trophic webs. Yet, global-scale diversity patterns of subterranean spiders are still mostly unknown. In the frame of the CAWEB project, a European joint network of cave arachnologists, we collected data on...

In light of recent alarming trends in human population growth, climate change, and other environmental modifications, a "Warning to humanity" manifesto was published in BioScience in 2017. This call reiterated most of the ideas originally expressed by the Union of Concerned Scientists in 1992, including the fear that we are "pushing Earth's ecosyst...

Gorski kotar je biospeleološki jedno od najslabije istraženih krških dijelova Hrvatske, stoga su sva istraživanja provedena na ovom području iznimno vrijedna. Fauna je sakupljana za vrijeme speleoloških ekspedicija u sjeverozapadnom dijelu Gorskog kotara tzv. „Šverdi“ u srpnju 2005., lipnju i srpnju 2006, u jednom navratu u lipnju 2011, te lipnju 2...

Because of their size, abundance and active predatory lifestyle, spiders of the family Dysderidae are among the most conspicuous creatures in the Dinaric caves. Historically, the interest for this group dates back to 1847, to the description of the first cave spider in the world, Stalita taenaria , and peaks in the middle of 20 th century with the...

Biokovo Mountain in Croatia is a Dinaric hotspot of subterranean biodiversity and its area of 196 km 2 is protected as a nature park. Until now, more than 400 caves have been registered here, however, only in about 30% of them biospeleological research has been carried out. It is hypothesized that over 1000 caves exist in highly karstified Biokovo...

Biokovo Mountain in Croatia is a Dinaric hotspot of subterranean biodiversity and its area of 196 km2 is protected as a nature park. Until now, more than 400 caves have been registered here, however, only in about 30 % of them biospeleological research has been carried out. It is hypothesized that over 1000 caves exist in highly karstified Biokovo...

We provide the first overview on spiders living in subterranean habitats in Europe, including the first European subterranean spider checklist. In Europe, there are 486 spider species known to dwell in caves and other subterranean habitats, distributed across 22 families. Despite a few species being able to colonize caves across the whole continent...

This paper describes and illustrates a new genus and a new species belonging to the family Nesticidae based on morphology and supported by molecular data. The new genus, Kryptonesticus gen. nov., groups eight species spread from Bulgaria and Turkey to Croatia, including Montenegro, Bosnia and Herzegovina and Crete. As a result, seven new combinatio...

The genus Troglocladius Andersen, Baranov et Hagenlund, gen. n. is erected based on T. hajdi Andersen, Baranov et Hagenlund, sp. n. collected at 980 m depth in the Lukina jama-Trojama cave system in Croatia. Morphological features such as pale color, strongly reduced eyes and very long legs make it a typical cave animal. Surprisingly, it has also r...

DNA extraction protocol for the specimens of Troglocladius hajdi Andersen, Baranov et Hagenlund, gen. nov., sp. nov. (DOCX)

Concatenated alignment for all the molecular markers used in the analysis. (DOCX)

Master mix for PCR and PCR thermocycling protocols for the genetic markers used in the analysis. (DOCX)

GenBank accession numbers for vouchers LH01 and LH02 of Troglocladius hajdi Andersen, Baranov et Hagenlund, gen. nov., sp. nov. (DOCX)

Reference sequence with secondary structure annotation for the alignment of 18S rDNA. (DOCX)

Although satellite DNAs are well-explored components of heterochromatin and centromeres, little is known about emergence, dispersal and possible impact of comparably structured tandem repeats (TRs) on the genome-wide scale. Our bioinformatics analysis of assembled Tribolium castaneum genome disclosed significant contribution of TRs in euchromatic c...

Transposable elements (TEs) and satellite DNAs (satDNAs) are typically identified as major repetitive DNA components in eukaryotic genomes. TEs are DNA segments able to move throughout a genome while satDNAs are tandemly repeated sequences organized in long arrays. Both classes of repetitive sequences are extremely diverse, and many TEs and satDNAs...

Tandemly arrayed non-coding sequences or satellite DNAs (satDNAs) are rapidly evolving segments of eukaryotic genomes, including the centromere, and may raise a genetic barrier that leads to speciation. However, determinants and mechanisms of satDNA sequence dynamics are only partially understood. Sequence analyses of a library of five satDNAs comm...

In this paper 5 species of cave-dwelling spiders of the genus Troglohyphantes are listed as new for the Croatian fauna. They are T. troglodytes (Kulczyñski, 1914), T. pugnax Deeleman-Reinhold, 1978, T. salax (Kulczyñski, 1914), T. sketi Deeleman-Reinhold, 1978 and T. subalpinus Thaler, 1967. All five species are known from neighboring countries. Ne...