Global Phylogeny Research Articles

AVOTREX: A Global Dataset of Extinct Birds and Their Traits

ABSTRACTMotivationHuman activities have been reshaping the natural world for tens of thousands of years, leading to the extinction of hundreds of bird species. Past research has provided evidence of extinction selectivity towards certain groups of species, but trait information is lacking for the majority of clades, especially for prehistoric extinctions identified only through subfossil remains. This incomplete knowledge potentially obscures the structure of natural communities, undermining our ability to infer changes in biodiversity across space and time, including trends in functional and phylogenetic diversity. Biases in currently available trait data also limit our ability to identify drivers and processes of extinction. Here we present AVOTREX, an open‐access database of species traits for all birds known to have gone extinct in the last 130,000 years. This database provides detailed morphological information for 610 extinct species, along with a pipeline to build phylogenetic trees that include these extinct species.Main Types of Variables ContainedFor each extinct bird species, we provide information on the taxonomy, geographic location, and period of extinction. We also present data on island endemicity, flight ability, and body mass, as well as standard measurements of external (matching the AVONET database of extant birds) and skeletal morphology from museum specimens where available. To ensure comprehensive morphological data coverage, we estimate all missing morphological measurements using a data imputation technique based on machine learning. Finally, we provide an R package to graft all extinct species onto a global phylogeny of extant species (BirdTree).Spatial Location and GrainGlobal.Time Period and GrainAll known globally extinct bird species from 130,000 years ago up until 2024.Major Taxa and Level of MeasurementBirds (Class Aves), species level.Software FormatSpreadsheets (.csv) stored in Dryad.

Evolutionary isolation of Canadian terrestrial vertebrate species

Conservation prioritization has become increasingly important as a practical response to ongoing biodiversity loss and limited resources. One tool, evolutionary distinctiveness (ED) is based on a measure of evolutionary isolation and has merit for identifying taxa with few close relatives. Here we present the first ever national-level ED scores for any jurisdiction, applying the measures to all Canadian tetrapods. We updated and pruned global dated phylogenies of all terrestrial vertebrates (amphibians, squamates, turtles, mammals, and birds) down to native Canadian species and calculated Canadian ED scores and rankings for each and compared them to their global ED ranks. Canada’s terrestrial ectotherm vertebrates (amphibians and reptiles) include most of Canada’s most evolutionarily isolated species and many score and rank higher nationally than globally in their ED scores. These taxa are also the most imperilled in Canada and so species with populations assessed as at-risk by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC) represent, on average, more than expected national evolutionary history. Interestingly, several exotic species also have very high national ED scores. To the extent that evolutionary isolation captures aspects of local and national biodiversity worth preserving, our lists may provide useful input to conservation agencies engaging in conservation prioritization exercises.

Nomenclatural revision of Celtis (Cannabaceae) described for northern South America, Central America, the Caribbean and the southern United States

In preparation for a taxonomic review and a global phylogeny focusing on the Neotropical lineages of Celtis, the names described to northern South America, the Caribbean, Central America and southern United States were revised. For the northern axis, 87 names were identified, 60 of which have been reviewed in this contribution. Lectotypes are designated for Celtis berlandieri, C. dichotoma, C. jamaicensis, C. litoralis, C. pavonii, C. pubescens, C. riparia, C. rufescens, C. schiedeana, C. swartzii, C. tikalana, C. triflora, C. velutina and Sponia chichilea. Neotypes were assigned to C. berteroana and C. lamarckiana. Thirty-three names did not undergo changes in their typological status and five were excluded. Among the results, we highlight the (unpublished) location of the holotype of Celtis laevigata, as well as the designation of an epitype for this same species.

La anatomía de la raíz como evidencia filogenética para los helechos Cheilanthoides (Pteridaceae)

Background and aims: To our hypothesis on the evolutionary relationships of Cheilanthoid ferns, based on molecular data and partially on morphological and reproductive data, we add here a study of root anatomy in the genera of the subfamily occurring in South America. M&M: Root characters were analyzed anatomically in 48 South American species representing the 12 genera of Cheilanthoideae occurring in South America. Techniques of plant histology were used for anatomical analysis and tissue characterization. Characters with possible diagnostic value were identified and mapped on a molecular phylogeny of Cheilanthoideae based on three plastidial markers (rbcL, trnL-F and rps4). Results: The character "type of root cortex" showed a distribution of states that fit to the major clades or genera in the phylogeny of the subfamily. The homogeneous cortex state was plesiomorphic for Cheilanthoideae, whereas the heterogeneous bark state was acquired by some genera of the hemionitoid clade: Hemionitis and the genera of the Adiantopsis-Doryopteris clade (except Mineirella). In addition, we discuss the role of different tissues in the root mechanics of this group. Conclusions: The character "type of root cortex" could contribute to the characterization of genera and the generic assignment of confusing species in the classification of Cheilanthoideae. However, the complete resolution of the relationship of hemionitds clade in the global phylogeny of the subfamily is necessary.

Identifiability of speciation times under the multispecies coalescent

The advent of rapid and inexpensive sequencing technologies has necessitated the development of computationally efficient methods for analyzing sequence data for many genes simultaneously in a phylogenetic framework. The coalescent process is the most commonly used model for linking the underlying genealogies of individual genes with the global species-level phylogeny, but inference under the coalescent model is computationally daunting in the typical inference frameworks (e.g., the likelihood and Bayesian frameworks) due to the dimensionality of the space of both gene trees and species trees. Here we consider estimation of the branch lengths in fixed species trees with three or four taxa, and show that these branch lengths are identifiable. We also show that for three and four taxa simple estimators for the branch lengths can be derived based on observed site pattern frequencies. Properties of these estimators, such as their asymptotic variances and large-sample distributions, are examined, and performance of the estimators is assessed using simulation. Finally, we use these estimators to develop a hypothesis test that can be used to delimit species under the coalescent model for three or four putative taxa.

The Rediscovery of a Relict Unlocks the First Global Phylogeny of Whip Spiders (Amblypygi).

Asymmetrical rates of cladogenesis and extinction abound in the tree of life, resulting in numerous minute clades that are dwarfed by larger sister groups. Such taxa are commonly regarded as phylogenetic relicts or "living fossils" when they exhibit an ancient first appearance in the fossil record and prolonged external morphological stasis, particularly in comparison to their more diversified sister groups. Due to their special status, various phylogenetic relicts tend to be well-studied and prioritized for conservation. A notable exception to this trend is found within Amblypygi ("whip spiders"), a visually striking order of functionally hexapodous arachnids that are notable for their antenniform first walking leg pair (the eponymous "whips"). Paleoamblypygi, the putative sister group to the remaining Amblypygi, is known from Late Carboniferous and Eocene deposits but is survived by a single living species, Paracharon caecusHansen (1921), that was last collected in 1899. Due to the absence of genomic sequence-grade tissue for this vital taxon, there is no global molecular phylogeny for Amblypygi to date, nor a fossil-calibrated estimation of divergences within the group. Here, we report a previously unknown species of Paleoamblypygi from a cave site in Colombia. Capitalizing upon this discovery, we generated the first molecular phylogeny of Amblypygi, integrating ultraconserved element sequencing with legacy Sanger datasets and including described extant genera. To quantify the impact of sampling Paleoamblypygi on divergence time estimation, we performed in silico experiments with pruning of Paracharon. We demonstrate that the omission of relicts has a significant impact on the accuracy of node dating approaches that outweighs the impact of excluding ingroup fossils, which bears upon the ancestral range reconstruction for the group. Our results underscore the imperative for biodiversity discovery efforts in elucidating the phylogenetic relationships of "dark taxa," and especially phylogenetic relicts in tropical and subtropical habitats. The lack of reciprocal monophyly for Charontidae and Charinidae leads us to subsume them into one family, Charontidae, new synonymy.

Taxonomy and phylogeny of the family Suberitidae (Porifera: Demospongiae) in California

This study presents a comprehensive taxonomic revision of the family Suberitidae (Porifera: Demospongiae) for California, USA. We include the three species previously known from the region, document two additional species previously known from other regions, and formally describe four new species as Pseudosuberites latke sp. nov., Suberites californiana sp. nov., Suberites kumeyaay sp. nov., and Suberites agaricus sp. nov. Multi-locus DNA sequence data is presented for seven of the nine species, and was combined with all publicly available data to produce the most comprehensive global phylogeny for the family to date. By integrating morphological and genetic data, we show that morphological characters may be sufficient for regional species identification but are likely inadequate for global classification into genera that reflect the evolutionary history of the family. We therefore propose that DNA sequencing is a critical component to support future taxonomic revisions.

Positive selection underlies repeated knockout of ORF8 in SARS-CoV-2 evolution

Knockout of the ORF8 protein has repeatedly spread through the global viral population during SARS-CoV-2 evolution. Here we use both regional and global pathogen sequencing to explore the selection pressures underlying its loss. In Washington State, we identified transmission clusters with ORF8 knockout throughout SARS-CoV-2 evolution, not just on novel, high fitness viral backbones. Indeed, ORF8 is truncated more frequently and knockouts circulate for longer than for any other gene. Using a global phylogeny, we find evidence of positive selection to explain this phenomenon: nonsense mutations resulting in shortened protein products occur more frequently and are associated with faster clade growth rates than synonymous mutations in ORF8. Loss of ORF8 is also associated with reduced clinical severity, highlighting the diverse clinical impacts of SARS-CoV-2 evolution.

Large-scale genome-wide SNP analysis reveals the rugged (and ragged) landscape of global ancestry, phylogeny, and demographic history in chicken breeds.

The worldwide chicken gene pool encompasses a remarkable, but shrinking, number of divergently selected breeds of diverse origin. This study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture, genetic variability, and detailed structure among 49 populations. These populations represent a significant sample of the world's chicken breeds from Europe (Russia, Czech Republic, France, Spain, UK, etc.), Asia (China), North America (USA), and Oceania (Australia). Based on the results of breed genotyping using the Illumina 60K single nucleotide polymorphism (SNP) chip, a bioinformatic analysis was carried out. This included the calculation of heterozygosity/homozygosity statistics, inbreeding coefficients, and effective population size. It also included assessment of linkage disequilibrium and construction of phylogenetic trees. Using multidimensional scaling, principal component analysis, and ADMIXTURE-assisted global ancestry analysis, we explored the genetic structure of populations and subpopulations in each breed. An overall 49-population phylogeny analysis was also performed, and a refined evolutionary model of chicken breed formation was proposed, which included egg, meat, dual-purpose types, and ambiguous breeds. Such a large-scale survey of genetic resources in poultry farming using modern genomic methods is of great interest both from the viewpoint of a general understanding of the genetics of the domestic chicken and for the further development of genomic technologies and approaches in poultry breeding. In general, whole genome SNP genotyping of promising chicken breeds from the worldwide gene pool will promote the further development of modern genomic science as applied to poultry.

Species richness in Myotis (Chiroptera: Vespertilionidae): species delimitation and expanded geographic sampling reveal high Neotropical diversity

Abstract With up to 137 species worldwide, Myotis,— a genus of small, insectivorous bats are an example for understanding biogeographic and evolutionary processes such as intercontinental colonization, diversification, speciation, and convergent adaptive evolution. Species limits and associated distributions, however, remain poorly delineated across significant portions of this diverse group and encompassing a vast geographic range. Here, we explore how diversity is partitioned across this radiation with a focus on Neotropical species of Myotis, using a barcoding approach (706 bp of the mitochondrial DNA gene cytochrome-b) that includes 544 individual sequences (116 newly generated sequences and 428 sequences from GenBank, including outgroups). Single-locus molecular barcoding is useful for identifying cryptic diversity and establishing hypotheses that can guide investigations of species boundaries and phylogenetic relationships, an especially important initial step in assessing poorly characterized, diverse clades. The global phylogeny produced from these data is consistent with the hypothesized monophyly of the New World clade and places the evolutionary relationships of Neotropical species of Myotis within the context of the Palearctic and Nearctic clades. We then explore species boundaries for 25 of the 36 nominal species of Neotropical Myotis, using 3 alternative species delimitation approaches (1 distance-based ABGD [Automatic Barcode Gap Discovery]; and 2 coalescent-based mPTP [multi-rate Poisson Tree Processes], GMYC [Generalized Mixed Yule Coalescent] model). The mPTP (n = 29 species) and ABGD (n = 26) approaches inferred different numbers of species than that recognized by current Neotropical Myotis taxonomy, whereas GMYC (n = 25) inferred the same number of species. In addition to the original 36 Neotropical nominal species currently recognized, we suggest that taxonomic revisions are needed to assess whether M. oxyotus gardneri and M. nigricans osculatii should be elevated to the species level and whether M. dinellii is distinct from M. levis. With the 7 potentially cryptic species identified herein that require further study, the number of Neotropical Myotis may approach 45 species. Taken together, our results suggest that rather than a classic example of a temperate radiation, there may be more species of Myotis in the Neotropics than Nearctic, Afrotropic, Indomalayan, and Oceanian Realms, with only the Palearctic region showing higher species richness.

Capitella (Annelida: Capitellidae) species in the Gulf of Mexico: Delimitation, phylogeography and phylogeny

AbstractCapitella spp. are found in marine and estuarine benthos world‐wide. They are often treated as environmental sentinels because they occur in high densities in areas of anthropogenic disturbance and organic pollution. However, there are many cryptic species around the world, often grouped into the Capitella capitata complex. Historically, these have been differentiated using allozymes and developmental studies. Recently, single‐gene sequencing, especially cytochrome c oxidase subunit I, and phylogenetic methods have been used to characterise populations around the world. We present molecular support and provide descriptions for five new Capitella spp. from the Gulf of Mexico: Capitella gomexa sp. n., Capitella mandingensis sp. n., Capitella tampe sp. n., Capitella maculosa sp. n. and Capitella loucindae sp. n. Two were recently differentiated on the basis of larval development and morphology. Additionally, we present an updated look at global Capitella phylogeny. While no apparent patterns of phylogeography were recovered, we did find support for a single origin of thoracic acicular spines.

The first record of Trichomanes s.s. (Hymenophyllaceae) in Asia and establishment of the new subgenus Asiatrichomanes

Callistopteris superba is a peculiar Asian species within the genus Callistopteris (Hymenophyllaceae). A detailed morphological study of available herbarium specimens was conducted and the species was integrated into a global molecular phylogeny of the family in order to more precisely investigate its taxonomy. Morphological analysis and dated phylogenetic reconstructions demonstrate that the species is not part of Callistopteris and is instead strongly supported as being included in the distinct genus Trichomanes, comprising mainly Neotropical and some Afro-Malagasy species. The uniqueness, within the Hymenophyllaceae and the genus Trichomanes, of an indumentum of glandular-like hairs on the adaxial side of the lamina and on the indusia, allows us to propose Asiatrichomanes as a new subgenus based on this species, which is here also neotypified.

Global phylogenetic analysis of soybean dwarf virus isolates and their associations with aphid vectors and severe disease in soybeans.

Soybean dwarf virus (SbDV) was first described in Japan as an agent of severe soybean disease transmitted by the foxglove aphid, Aulacorthum solani, with separable yellowing (Y) and dwarfing (D) strains. SbDV of both Y and D genotypes were later documented in other countries. For three decades, SbDV isolates were assessed to evaluate risk to U.S. soybean production. U.S. SbDV isolates were transmitted by the pea aphid Acyrthosiphum pisum and showed limited disease in soybeans, suggesting it was not a major threat to U.S. soybean production. Here we report 21 new full-length SbDV genome sequences including those of the originally described Japanese Y and D isolates, isolates from Syria and New Zealand associated with severe disease, and 17 isolates from U.S. field collections. Using these new full-length genomes, a global phylogeny was assembled and used to revisit risk assessment based on sequence similarities, isolate pathogenicity, and vector specificity.

The Place of S Genotype of Mycobacterium Tuberculosis Which is Endemic to the Republic of Sakha (Yakutia), in the Global Phylogeny according to Results of Whole-Genome Sequencing

The objective: to assess the stability of circulation of S genotype and S-like strains of M. tuberculosis (MTB) in the Republic of Sakha (Yakutia) over a 12-year period and perform their phylogenetic identification relative to the L4.4 Euro-American subline.Subjects and Methods. Between 2009 and 2022, 513 MTB strains isolated from pulmonary tuberculosis patients were studied using molecular genetic methods. 92 isolates belonging to S genotype or having an S-like genetic profile were found. Whole-genome sequencing of five strains of S genotype that circulated in the territory of the Republic of Sakha (Yakutia) in 2020-2022 was carried out. A global phylogenetic analysis was performed and evolutionary relationship of the obtained genomes was determined, a RT-PCR test was developed for the rapid detection of S genotype strains.Results. In the territory of the Republic of Sakha (Yakutia), there is a stable circulation of S and S-like MTB genotypes belonging to the L4.4 Euro-American subline, the L4.4.1.1 subtype. The evolutionary model has confirmed the previously stated hypothesis that the spread of the S genotype among the indigenous population of Yakutia is associated with mass exposure to the Russian settlers which started from the beginning of the 17th century.Conclusion. Spread of MTB strains of the L4.4 Euro-American subline, L4.4.1.1 subtype, among the indigenous populations of New Zealand, Canada and Yakutia in the 17th-19th centuries is very similar.

Systematics of deep-sea starfish order Brisingida (Echinodermata: Asteroidea), with a revised classification and assessments of morphological characters

Brisingida Fisher 1928 is one of the seven currently recognised starfish orders, and one of the least known taxa as being exclusive deep-sea inhabitants. Modern deep-sea expeditions revealed their common occurrences in various deep-sea settings including seamounts, basins and hydrothermal vent peripheral, underlining the necessity of clarifying their global diversity and phylogeny. In this study, we present a comprehensive molecular phylogeny of Brisingida which encompasses the highest taxonomic diversity to date. DNA sequences (COI, 16S, 12S and 28S) were obtained from 225 specimens collected in the global ocean, identified as 58 species spanning 15 of the 17 extant genera. Phylogenetic relationship was inferred using both maximum likelihood and Bayesian inference methods, revealing polyphyletic families and genera and indicating nonnegligible bias in prior morphology-based systematics. Based on the new phylogeny, a novel classification of the order, consisting of 5 families and 17 genera, is proposed. Families Odinellidae, Brisingasteridae and Novodiniidae (sensu Clark and Mah, 2001) were resurrected to encompass the genera Odinella, Brisingaster and Novodinia. Brisingidae and Freyellidae were revised to include 11 and 3 genera, respectively. A new genus and species, two new subgenera and seven new combinations are described and a key to each genus and family is provided. Transformations of morphological traits were evaluated under the present phylogenetic hypothesis. A series of paedomorphic characters were found in many genera and species, which led to a high degree of homoplasy across phylogenetically distant groups. Our results provide new insights in the phylogeny and ontogeny of the order, and highlight the necessity to evaluate character convergence under sound phylogenetic hypothesis.

Phylogenetic and functional analyses of N6-methyladenosine RNA methylation factors in the wheat scab fungus Fusarium graminearum.

In eukaryotes, N6-methyladenosine (m6A) RNA modification plays a crucial role in governing the fate of RNA molecules and has been linked to various developmental processes. However, the phyletic distribution and functions of genetic factors responsible for m6A modification remain largely unexplored in fungi. To get insights into the evolution of m6A machineries, we reconstructed global phylogenies of potential m6A writers, readers, and erasers in fungi. Substantial copy number variations were observed, ranging from up to five m6A writers in early-diverging fungi to a single copy in the subphylum Pezizomycotina, which primarily comprises filamentous fungi. To characterize m6A factors in a phytopathogenic fungus Fusarium graminearum, we generated knockout mutants lacking potential m6A factors including the sole m6A writer MTA1. However, the resulting knockouts did not exhibit any noticeable phenotypic changes during vegetative and sexual growth stages. As obtaining a homozygous knockout lacking MTA1 was likely hindered by its essential role, we generated MTA1-overexpressing strains (MTA1-OE). The MTA1-OE5 strain showed delayed conidial germination and reduced hyphal branching, suggesting its involvement during vegetative growth. Consistent with these findings, the expression levels of MTA1 and a potential m6A reader YTH1 were dramatically induced in germinating conidia, followed by the expression of potential m6A erasers at later vegetative stages. Several genes including transcription factors, transporters, and various enzymes were found to be significantly upregulated and downregulated in the MTA1-OE5 strain. Overall, our study highlights the functional importance of the m6A methylation during conidial germination in F. graminearum and provides a foundation for future investigations into m6A modification sites in filamentous fungi.IMPORTANCEN6-methyladenosine (m6A) RNA methylation is a reversible posttranscriptional modification that regulates RNA function and plays a crucial role in diverse developmental processes. This study addresses the knowledge gap regarding phyletic distribution and functions of m6A factors in fungi. The identification of copy number variations among fungal groups enriches our knowledge regarding the evolution of m6A machinery in fungi. Functional characterization of m6A factors in a phytopathogenic filamentous fungus Fusarium graminearum provides insights into the essential role of the m6A writer MTA1 in conidial germination and hyphal branching. The observed effects of overexpressing MTA1 on fungal growth and gene expression patterns of m6A factors throughout the life cycle of F. graminearum further underscore the importance of m6A modification in conidial germination. Overall, this study significantly advances our understanding of m6A modification in fungi, paving the way for future research into its roles in filamentous growth and potential applications in disease control.

Global phylogenomic diversity of Brucella abortus: spread of a dominant lineage

Brucella abortus is a globally important zoonotic pathogen largely found in cattle hosts and is typically transmitted to humans through contaminated dairy products or contact with diseased animals. Despite the long, shared history of cattle and humans, little is known about how trade in cattle has spread this pathogen throughout the world. Whole genome sequencing provides unparalleled resolution to investigate the global evolutionary history of a bacterium such as B. abortus by providing phylogenetic resolution that has been unobtainable using other methods. We report on large-scale genome sequencing and analysis of B. abortus collected globally from cattle and 16 other hosts from 52 countries. We used single nucleotide polymorphisms (SNPs) to identify genetic variation in 1,074 B. abortus genomes and using maximum parsimony generated a phylogeny that identified four major clades. Two of these clades, clade A (median date 972 CE; 95% HPD, 781–1142 CE) and clade B (median date 150 BCE; 95% HPD, 515 BCE–164 CE), were exceptionally diverse for this species and are exclusively of African origin where provenance is known. The third clade, clade C (median date 949 CE; 95% HPD, 766–1102 CE), had most isolates coming from a broad swath of the Middle East, Europe, and Asia, also had relatively high diversity. Finally, the fourth major clade, clade D (median date 1467 CE; 95% HPD, 1367–1553 CE) comprises the large majority of genomes in a dominant but relatively monomorphic group that predominantly infects cattle in Europe and the Americas. These data are consistent with an African origin for B. abortus and a subsequent spread to the Middle East, Europe, and Asia, probably through the movement of infected cattle. We hypothesize that European arrival to the Americas starting in the 15th century introduced B. abortus from Western Europe through the introduction of a few common cattle breeds infected with strains from clade D. These data provide the foundation of a comprehensive global phylogeny of this important zoonotic pathogen that should be an important resource in human and veterinary epidemiology.

Widespread arboreal foraging behavior in ground-dwelling birds and the urgency of life-history studies

Habitat changes can alter animal behaviors, especially of large-bodied animals. Landfowl (Galliformes) are a phylogenetically diverse group of large-bodied ground-dwelling birds that are generally considered reluctant flyers. However, some species of landfowl have also been found to forage in arboreal habitats, which could be particularly advantageous under declining habitat quality. However, the prevalence of arboreal foraging behavior (AFB) and how it relates to habitat changes are still unexplored. Here, we reviewed life-history traits associated with foraging behaviors in 305 species of landfowl worldwide and examined the prevalence of AFB across the global landfowl phylogeny. We also collected data from arboreal camera traps on 22 subtropical reservoir islands and six nearby mainland sites in the Thousand Island Lake region of China to assess AFB of Silver Pheasant (Lophura nycthemera), the largest landfowl in this lake system, with island area and isolation. Globally, at least 84 species of landfowl (28%) showed evidence of AFB, with a strong phylogenetic signal. Camera trapping revealed that Silver Pheasant tended to have AFB on small and isolated islands, as evidenced by the increased arboreal sampling efforts. Our study reveals that landfowl’s AFB is much more widespread than previously recognized, and suggests the importance of prioritizing large, connected habitats for the conservation of large-bodied animals like Silver Pheasant in the fragmented landscape. Finally, camera trapping emerges as a promising tool for recording landfowl’s life history and uncommon behaviors that can help us understand landfowl’s threats and aid conservation programs.

Refining the Global Phylogeny of Mitochondrial N1a, X, and HV2 Haplogroups Based on Rare Mitogenomes from Croatian Isolates.

Mitochondrial DNA (mtDNA) has been used for decades as a predominant tool in population genetics and as a valuable addition to forensic genetic research, owing to its unique maternal inheritance pattern that enables the tracing of individuals along the maternal lineage across numerous generations. The dynamic interplay between evolutionary forces, primarily genetic drift, bottlenecks, and the founder effect, can exert significant influence on genetic profiles. Consequently, the Adriatic islands have accumulated a subset of lineages that exhibits remarkable absence or rarity within other European populations. This distinctive genetic composition underscores the islands' potential as a significant resource in phylogenetic research, with implications reaching beyond regional boundaries to contribute to a global understanding. In the initial attempt to expand the mitochondrial forensic database of the Croatian population with haplotypes from small isolated communities, we sequenced mitogenomes of rare haplogroups from different Croatian island and mainland populations using next-generation sequencing (NGS). In the next step and based on the obtained results, we refined the global phylogeny of haplogroup N1a, HV2, and X by analyzing rare haplotypes, which are absent from the current phylogenetic tree. The trees were based on 16 novel and 52 previously published samples, revealing completely novel branches in the X and HV2 haplogroups and a new European cluster in the ancestral N1a variant, previously believed to be an exclusively African-Asian haplogroup. The research emphasizes the importance of investigating geographically isolated populations and their unique characteristics within a global context.

Quantifying and overcoming Darwinian shortfalls to conserve the fish tree of life

Knowledge shortfalls of the evolutionary history of bony fishes hamper phylogenetically informed conservation approaches. To direct future research efforts and phylogenetically based conservation actions, we calculated Darwinian shortfalls for taxonomic clades (genus, family and order-level) and countries, as well as derived a phylogenetic based prioritization metric for bony fishes. We built a synthesis phylogeny for 32,870 bony fishes using a global backbone phylogeny and inserting absent species by their taxonomic hierarchies (supertree approach). Then, we quantified knowledge shortfalls as the sum of inserted branch lengths divided by the total sum of branch lengths. The Darwinian shortfall was generally higher in diverse clades and countries with the lowest gross domestic product per capita and higher number of species and proportion of freshwater species. Clades and countries with the highest deficits should be prioritized for future research efforts, such as the Gymnotiformes from Brazil. By weighing species' evolutionary distinctiveness and vulnerability, we highlighted species that should be prioritized for best conserving the fish tree of life. Our study provides an open-data framework for prioritizing future efforts toward advancing biodiversity knowledge and conservation.