Phylogeographic Research Articles

Phylogenomics, reticulation, and biogeographical history of Elaeagnaceae

The angiosperm family Elaeagnaceae comprises three genera and ca. 100 species distributed mainly in Eurasia and North America. Little family-wide phylogenetic and biogeographic research on Elaeagnaceae has been conducted, limiting the application and preservation of natural genetic resources. Here, we reconstructed a strongly supported phylogenetic framework of Elaeagnaceae to better understand inter- and intrageneric relationships, as well as the origin and biogeographical history of the family. For this purpose, we used both nuclear and plastid sequences from Hyb-Seq and genome skimming approaches to reconstruct a well-supported phylogeny and, along with current distributional data, infer historical biogeographical processes. Our phylogenetic analyses of both nuclear and plastid data strongly support the monophyly of Elaeagnaceae and each of the three genera. Elaeagnus was resolved as sister to the well-supported clade of Hippophae and Shepherdia. The intrageneric relationships of Elaeagnus and Hippophae were also well resolved. High levels of nuclear gene tree conflict and cytonuclear discordance were detected within Elaeagnus, and our analyses suggest putative ancient and recent hybridization. We inferred that Elaeagnaceae originated at ca. 90.48 Ma (95% CI = 89.91–91.05 Ma), and long-distance dispersal likely played a major role in shaping its intercontinentally disjunct distribution. This work presents the most comprehensive phylogenetic framework for Elaeagnaceae to date, offers new insights into previously unresolved relationships in Elaeagnus, and provides a foundation for further studies on classification, evolution, biogeography, and conservation of Elaeagnaceae.

“Fossil woods from the Miocene of Costa Rica and Nicaragua: Insights into the Neotropical floral puzzle”

The fossil record of Central America plays a pivotal role in our comprehensive understanding of the Neotropical Flora. It represents a mosaic of elements from South America that migrated to North America and vice versa, contributing to the rich diversity of flora we observe today. Despite the importance of Central America's vegetation history, our knowledge remains fragmented, with limited information available for regions like Costa Rica and Nicaragua. This study presents findings based on the first five wood samples collected from Miocene sites in Costa Rica and Nicaragua, situated across slopes ranging from 10 to 1000 m above sea level, reminiscent of tropical environments. These specimens exhibit common characteristics such as a median vessel element diameter of 100–200 μm, small to medium - sized alternate inter - vessel pits, relatively thin and slightly heterogeneous rays spanning 1 to 3 cells in thickness, and a prevalence of procumbent cells. Additionally, we observed vasicentric and thin - banded axial parenchyma, thin - walled fibers, and the presence of few gums and tyloses. The variability in these features suggests the presence of taxa belonging to families such as Sapotaceae (cf. Vitellaria), Leguminosae (cf. Aphanocalyx and cf. Dalbergia), Malvaceae/Sterculiodeiae (cf. Cola), and Myrtaceae (cf. Eucalyptus), most of which have been reported in both North and South America. Therefore, understanding the timing of their arrival and their biogeographic histories is crucial for elucidating the origins and composition of today's Neotropical Flora. Our findings challenge the simplistic narrative of recent migration from southern and northern floras shaping the Neotropical Flora. Instead, they underscore the complexity of its evolutionary history, highlighting the intricate interplay of various taxa over time to generate this unique tropical assemblage.

Phylogenetics and biogeography of the olive family (Oleaceae).

Progress in the systematic studies of the olive family (Oleaceae) during the last two decades provides the opportunity to update its backbone phylogeny and to investigate its historical biogeography. We additionally aimed to understand the factors underlying the disjunct distribution pattern between East Asia and both West Asia and Europe that is found more commonly in this family than in any other woody plant families. Using a sampling of 298 species out of ca. 750, the largest in a phylogenetic study of Oleaceae thus far, and a set of 36 plastid and nuclear markers, we reconstructed and dated a new phylogenetic tree based on maximum likelihood and Bayesian methods and checked for any reticulation events. We also assessed the relative support of four competing hypotheses [Qinghai-Tibet Plateau uplift (QTP-only hypothesis), climatic fluctuations (Climate-only hypothesis), combined effects of QTP uplift and climate (QTP-Climate hypothesis), and no effects (Null hypothesis)] in explaining these disjunct distributions. We recovered all tribes and subtribes within Oleaceae as monophyletic, but uncertainty in the position of tribe Forsythieae remains. Based on this dataset, no reticulation event was detected. Our biogeographic analyses support the QTP-Climate hypothesis as the likely main explanation for the East-West Eurasian disjunctions in Oleaceae. Our results also show an earlier origin of Oleaceae at ca. 86 Mya and the role of Tropical Asia as a main source of species dispersals. Our new family-wide and extensive phylogenetic tree highlights both the stable relationships within Oleaceae, including the polyphyly of the genus Chionanthus, and the need for further systematic studies within the family's largest and most under-sampled genera (Chionanthus and Jasminum). Increased sampling will also help to fine-tune biogeographic analyses across spatial scales and geological times.

A new perspective on the molecular dating of the stone crayfish with an extended phylogeographic information on the species

Reconstructing the origin and historical biogeography of the Austropotamobius torrentium is hampered by insufficient phylogeographic coverage of the Balkans and deep contradictions in previous molecular dating. The present work extends the phylogeographic coverage to Serbia, a country crucial for understanding the species southward dispersal. Our analysis revealed that the Southern Balkans lineage occurs in most of the country, the Central and southeastern Europe lineage is restricted to the southwest and northeast of the country, while a single population in the north of the country harbors the Lika and Dalmatia lineage, which was previously thought to be restricted to the northern-central Dinarides. Dataset expansion led to revised phylogenetic relationships, which indicated that the Apuseni lineage is not nested within Northern-central Dinarides lineages but arose after the most basal split within Austropotamobius torrentium. This ‘Apuseni first’ phylogeny provides a new perspective for molecular dating, according to which the split between Austropotamobius pallipes and A. torrentium took place in the Late Oligocene, while the formation of the phyletic lineages and the dispersal from the Dinarides to Serbia occurred in the late Miocene and is probably associated with the complex and protracted process of disintegration of the Neogene freshwater lakes in southeastern Europe.

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The Zagros Mountain range in western Iran is an area of species endemism within the Irano-Anatolian biodiversity hotspot. A couple of relict and morphologically isolated species have been reported for the Zagros Mountains, yet their distribution patterns in relation to the geological and climatic history of the region are not fully understood. Clinopodium kallaricum (Jamzad) Bordbar, 2019 (Lamiaceae), Hypericum dogonbadanicum Assadi, 1984 (Hypericaceae), and Iranoaster bachtiaricus (Mozaff.) Kaz. Osaloo, Farhani & Mozaff. 2018 (Asteraceae) are local endemic species restricted to Zagros with no clear affinities to the Irano-Turanian or other Northern Hemisphere temperate species. Previous studies suggested some afromontane relations for these species, beyond the Saharo-Sindian lowlands. Here, we provide dated phylogenies for these three species, to assess the most probable drivers behind this pattern of distribution. Our results represent that the split between these taxa and their relatives is not contemporaneous, implying different biogeographical histories. I. bachtiaricus originated in the Middle Miocene, while C. kallaricum and H. dogonbadanicum are relatively younger (late Miocene early Pliocene). The divergence of these taxa coincided with the major geological and climatic events of the Miocene, mainly the collision of the Afro-Arabia and Eurasia plates in 18-16 Mya and the aridification of the Sahara (started in 11-7 Mya), followed by a shift in the vegetation of the Sahara from subtropical/steppe to arid desert. The possible relict nature of these species is discussed, and the role of the Saharo-Sindian Region as a vicariant agent is highlighted, which could have subdivided formerly uniform populations and subsequently accelerated the allopatric speciation.

The Asian rock-dwelling antlions Gatzara Navás, 1915 and Nepsalus Navás, 1914 (Neuroptera: Myrmeleontidae): new advancements in systematics, biogeography and life history.

The antlion genera Gatzara and Nepsalus (Myrmeleontidae: Dendroleontinae) inhabit mountain forests and are characterised by camouflaging larvae. Both genera remain poorly known despite recent findings on systematics and distribution. We report the discovery of new specimens and the previously unknown larvae of the rare species Gatzara jubilaea Navás, 1915, Nepsalus insolitus (Walker, 1860) and N. decorosus (Yang, 1988). These provide new evidence regarding the affinities of these species, and updated knowledge of the distribution, larval morphology and biology. Moreover, a new species of Nepsalus , N. maclachlani Badano, Zheng & Liu, sp. nov. is described from Sri Lanka based on historical museum collections. The discovery of the immature stages of Gatzara shows that the larvae of this genus share the same specialised ecological characteristics and habits as those of Nepsalus but are less morphologically derived. We also reconstruct a molecular phylogeny of this lineage, estimating the divergence time and biogeographical history by adding the new samples. The evolution of the Gatzara + Nepsalus lineage is associated with two major mountain ranges on the southern Tibetan Plateau, i.e. the Himalayas and the Hengduan Mountains. ZooBank: urn:lsid:zoobank.org:pub:68E68211-DFC1-4D98-997B-8A23BA8F9B69.

Total-evidence dating and the phylogenetic affinities of early fossil passerines

Passeriformes is the most diverse and globally widespread order of living birds. However, little work has been done on the phylogenetic relationships within their fossil record. Recent advances in total-evidence phylogenetic methods have improved topological and age estimation by using morphological, molecular and temporal data. This provides the opportunity to investigate the phylogenetic affinities of five recently described passerines from the early Oligocene of Europe, including some of the most complete and oldest passerine fossils described to date. We compare maximum parsimony, non-clock Bayesian inference, and total-evidence tip-dating Bayesian analysis to estimate relationships and divergence times of the fossil passerines. We find Wieslochia weissi, Crosnoornis nargizia and NT-LBR-0014 form a clade within Tyranni (suboscines) either in the stem or within Old-World suboscines (Eurylaimides). Jamna szybiaki is recovered as the sister lineage of crown Passeriformes. We confirmed the oscine affinities of Resoviaornis jamrozi. Its precise position within Passeri remains ambiguous, but affinities within Corvides or Passerides may be more likely considering the biogeographic history of the group. We emphasize the importance of an informative tree age prior in total-evidence dating analyses and appeal for the further development of models for phylogenetic inference using morphology.

Plastomes of Nothofagus reflect a shared biogeographic history in Patagonia.

Plastomes are used in phylogenetic reconstructions because of their relatively conserved nature. Nonetheless, some limitations arise, particularly at lower taxonomic levels due to reduced interspecific polymorphisms and frequent hybridization events that result in unsolved phylogenies including polytomies and reticulate evolutionary patterns. Next-generation sequencing technologies allow access to genomic data and strongly supported phylogenies, yet biased topologies may be obtained due to insufficient taxon sampling. We analyze the hypothesis that intraspecific plastome diversity reflects biogeographic history and hybridization cycles among taxa. We generated 12 new plastome sequences covering distinct latitudinal locations of all species of subgenus Nothofagus from North Patagonia. Chloroplast genomes were assembled, annotated, and searched for simple sequence repeats (SSRs). Phylogenetic reconstructions included species and sampled locations. The six Nothofagus species analyzed were of similar size and structure; only Nothofagus obliqua of subgenus Lophozonia, used as an outgroup, presented slight differences in size. We detected a variable number of SSRs in distinct species and locations. Phylogenetic analyses of plastomes confirmed that subgenus Nothofagus organizes into two monophyletic clades each consisting of individuals of different species. We detected a geographic structure within subgenus Nothofagus and found evidence of local chloroplast sharing due to past hybridization, followed by adaptive introgression and ecological divergence. These contributions enrich the comprehension of transversal evolutionary mechanisms such as chloroplast capture and its implications for phylogenetic and phylogenomic analyses.

Habitat opening fostered diversity: impact of dispersal and habitat‐shifts in the evolutionary history of a speciose afrotropical insect group

The opening of habitats associated with the emergence of C4 grasslands during the Neogene had a massive influence on the evolution of plant and animal communities. Strikingly, the impacts of grassland expansion on species diversification in Africa, where the largest surface of grasslands and savannas in the world is located, are not well understood. To explore the impact of habitat opening, we investigate the evolution of noctuid stemborers, a group of moths mostly associated with open habitats, and whose diversity is centered in the Afrotropics. We generate a dated molecular phylogeny for ca 80% of the known stemborer species, and assess the role of habitat opening on the evolutionary trajectory of the group through a combination of parametric historical biogeography, ancestral character state estimation, life history traits and habitat‐dependent diversification analyses. Our results support an origin of stemborers in Southern and East Africa ca 20 million years ago (Ma), with range expansions linked to the increased availability of open habitats to act as dispersal corridors, and closed habitats acting as potent barriers to dispersal. Early specialization on open habitats was maintained over time, with shifts towards closed habitats being rare and invariably unidirectional. Analyses of life history traits showed that habitat changes involved specific features likely associated with grassland adaptations, such as variations in larval behavior and color. We compare these findings to those previously inferred for an Afrotropical butterfly group that diversified roughly in parallel with the stemborers but distributed predominantly in closed habitats. Remarkably, these two groups show nearly opposite responses in relation to habitat specialization, whether in terms of biogeographical patterns, or in terms of rates of transition between open and closed habitats. We conclude that habitat opening played a major role in the evolutionary history of Afrotropical lineages through dispersal and adaptation linked to habitat shifts.

Macro- and micromorphology of Carex pauciflora-type fossils (Cyperaceae) from Europe and Siberia reveals unexpected affinity to Carex sect. Cyperoideae

Elongated biconvex Carex fossil fruits are relatively common in fossil assemblages, but they are of much uncertain taxonomic affinity. Three fossil-species have been erected to accommodate the materials from the respective type localities (C. klarae, C. paucifloriformis and C. paucifloroides) and a number of superficially similar-looking fossils were reported from other sites. The formerly proposed affinities mostly pointed to the extant C. pauciflora (subgen. Euthyceras) or Carex sect. Cyperoideae (subgen. Vignea), depending on the authors. But despite the similar superficial resemblance of the fossil remains to these not very closely related sedge taxa, other groups are also possible matches. We used a comparative approach employing stereomicroscope and SEM to analyze the affinities of several Old World “mummified” fossils (ca. 23 to 0.1 Ma) of elongated biconvex fruits. Several samples showed a fair preservation of previously unattested microscopic characters. In particular, one of them allowed us to detect an indirect record of fine silica body morphologies (impressions) on the periclinal walls, which permitted the sound taxonomic placement of the remains from the Miocene of Siberia as a Carex sect. Cyperoideae. In all the other fossils analyzed, the epidermal cell outline and the central position of the main silica body were sufficient to discard assignment to subgen. Euthyceras, despite a purported affinity to C. pauciflora reported in previous literature. In the absence of detailed information on silica bodies, epidermal cell (exocarp) details in fossil specimens do not seem to be determinant for the systematic placement. However, the addition of diagnostic style characters pointed to sect. Cyperoideae as the best match with the available information. Our data support a continued presence of Carex sect. Cyperoideae in the Old World since the Miocene, which candidates Eurasia as a possible place of origin for it, despite DNA-based reconstructions alone proposed North America. This study underlines the importance of detailed taxonomic studies to properly address the identity of fossils and unravel the biogeographic history of plants.

Limited evidence for genetic differentiation or adaptation in two amphibian species across replicated rural-urban gradients.

Urbanization leads to complex environmental changes and poses multiple challenges to organisms. Amphibians are highly susceptible to the effects of urbanization, with land use conversion, habitat destruction, and degradation ranked as the most significant threats. Consequently, amphibians are declining in urban areas, in both population numbers and abundance, however, the effect of urbanization on population genetic parameters remains unclear. Here, we studied the genomic response to urbanization in two widespread European species, the common toad Bufo bufo (26 localities, 480 individuals), and the smooth newt Lissotriton vulgaris (30 localities, 516 individuals) in three geographic regions: southern and northern Poland and southern Norway. We assessed genome-wide SNP variation using RADseq (ca. 42 and 552 thousand SNPs in toads and newts, respectively) and adaptively relevant major histocompatibility complex (MHC) class I and II genes. The results linked most of the genetic differentiation in both marker types to regional (latitudinal) effects, which also correspond to historical biogeography. Further, we did not find any association between genetic differentiation and level of urbanization at local scales for either species. However, urban smooth newts, but not toads, have lower levels of within-population genome-wide diversity, suggesting higher susceptibility to the negative effects of urbanization. A decreasing level of genetic diversity linked to increasing urbanization was also found for MHC II in smooth newts, while the relationship between MHC class I diversity and urbanization differed between geographic regions. We did not find any effects of urbanization on MHC diversity in the toad populations. Although two genetic environment association analyses of genome-wide data, LFMM and BayPass, revealed numerous (219 in B. bufo and 7040 in L. vulgaris) SNPs statistically associated with urbanization, we found a marked lack of repeatability between geographic regions, suggesting a complex and multifaceted response to natural selection elicited by life in the city.

Biogeography: A Case in Spatial Distribution Pattern of 21 Pinus thunbergii Populations in Japan

Abstract Biogeography is study of spatial distribution of organisms that has always been a source of fascination for naturalists, ecologists, and scientists. Evaluating genetic differentiation at various spatial scales provides valuable biogeographical insights relate to genetic structure of the species within the populations. The Expressed Sequence Tag - Simple Sequence Repeat, EST-SSR, marker used in these studies to gain insights into the efficiency of this marker. The objective of these studies was to provide a deeper understanding of the genetic diversity, structure, and phylogeographic history of this species, thus filling an important knowledge gap in the field of forest genetics and biogeography. According to historical context that cultivation and domestication of P. thunbergii have been taking place for centuries. Consequently, the spatial distribution pattern of 21 P. thunbergii populations cannot be divorced from the influence of human activities. It is provides valuable information about the factors that have led to the observed distribution pattern. Genetic differentiation has revealed distinct differences between two predecessor clusters, West-South Ward and East-North Ward. These clusters may hold insights into the biogeographical history of P. thunbergii in Japan, shedding light on its evolutionary past and how it has adapted to its environment over time.

Timing and direction of faunal exchange between the Nearctic and the Palaearctic in Odonata

AbstractAimSpecies have different distribution patterns across the globe and among biogeographical regions. The Nearctic and Palaearctic regions share lineages because of their parallel biogeographic histories and ecological conditions. As the number of phylogenetic studies increases, there are more insights into past exchange events between these two regions and their effects on the current distribution of diversity. However, several groups have not been tested and an overall generalization is still missing. Here, we analyse the biogeographic history across multiple genera of odonates to elucidate a general process of species exchange, vicariance and species divergence between these two regions.LocationThe Holarctic, including the entire Nearctic and the East and West Palaearctic.Taxon14 genera of Odonata (Insecta).MethodsWe reconstructed a time‐calibrated phylogenetic tree for each genus to determine species relationships and divergence time using 3614 COI sequences of 259 species. Biogeographic ancestral range estimation was inferred for each phylogeny using BioGeoBEARS. Preferred habitat (lotic versus lentic) was established for each species.ResultsExchange events were not restricted in time, direction or either lentic habitat or lotic habitat. Most genera crossed between both regions only once, and it was mainly across the Beringia, while three diverse anisopteran genera revealed multiple exchanges. Recent exchanges during the Pleistocene were associated with cold‐dwelling and lentic species.Main ConclusionsOur finding reveals the absence of a generalizable pattern of species exchange and divergence between the Nearctic and Palaearctic regions; instead, we found lineage‐specific biogeographic patterns. This finding highlights the complexity of drivers and functional traits that shaped current diversity patterns. Moreover, it emphasizes that general conclusions cannot be formulated based on one single clade.

The diverse liver viromes of Australian geckos and skinks are dominated by hepaciviruses and picornaviruses and reflect host taxonomy and habitat

Abstract Lizards have diverse ecologies and evolutionary histories, and represent a promising group to explore how hosts shape virome structure and virus evolution. Yet, little is known about the viromes of these animals. In Australia, squamates (lizards and snakes) comprise the most diverse order of vertebrates, and Australia hosts the highest diversity of lizards globally, with the greatest breadth of habitat use. We used meta-transcriptomic sequencing to determine the virome of nine co-distributed, tropical lizard species from three taxonomic families in Australia and analyzed these data to identify host traits associated with viral abundance and diversity. We show that lizards carry a large diversity of viruses, identifying more than thirty novel, highly divergent vertebrate-associated viruses. These viruses were from nine viral families, including several that contain well known pathogens, such as the Flaviviridae, Picornaviridae, Bornaviridae, Iridoviridae, and Rhabdoviridae. Members of the Flaviviridae were particularly abundant across species sampled here, largely belonging to the genus Hepacivirus: fourteen novel hepaciviruses were identified, broadening the known diversity of this group and better defining its evolution by uncovering new reptilian clades. The evolutionary histories of the viruses studied here frequently aligned with the biogeographic and phylogenetic histories of the hosts, indicating that exogenous viruses may help infer host evolutionary history if sampling is strategic and sampling density high enough. Notably, analysis of alpha and beta diversity revealed that virome composition and richness in the animals sampled here was shaped by host taxonomy and habitat. In sum, we identified a diverse range of reptile viruses that broadly contributes to our understanding of virus-host ecology and evolution.

Genome assembly of M. spongiola and comparative genomics of the genus Morchella provide initial insights into taxonomy and adaptive evolution.

Morchella spongiola is a highly prized mushroom for its delicious flavor and medical value and is one of the most flourishing, representative, and dominant macrofungi in the Qilian Mountains of the Qinghai-Tibet Plateau subkingdoms (QTPs). However, the understanding of M. spongiola remains largely unknown, and its taxonomy is ambiguous. In this study, we redescribed a unique species of M. spongiola, i.e., micromorphology, molecular data, genomics, and comparative genomics, and the historical biogeography of M. spongiola were estimated for 182 single-copy homologous genes. A high-quality chromosome-level reference genome of M. spongiola M12-10 was obtained by combining PacBio HiFi data and Illumina sequencing technologies; it was approximately 57.1Mb (contig N50 of 18.14Mb) and contained 9775 protein-coding genes. Comparative genome analysis revealed considerable conservation and unique characteristics between M. spongiola M12-10 and 32 other Morchella species. Molecular phylogenetic analysis indicated that M. spongiola M12-10 is similar to the M. prava/Mes-7 present in sandy soil near rivers, differentiating from black morels ~ 43.06 Mya (million years ago), and diverged from M. parva/Mes-7 at approximately 12.85 Mya (in the Miocene epoch), which is closely related to the geological activities in the QTPs (in the Neogene). Therefore, M. spongiola is a unique species rather than a synonym of M. vulgaris/Mes-5, which has a distinctive grey-brown sponge-like ascomata. This genome of M. spongiola M12-10 is the first published genome sequence of the species in the genus Morchella from the QTPs, which could aid future studies on functional gene identification, germplasm resource management, and molecular breeding efforts, as well as evolutionary studies on the Morchella taxon in the QTPs.

Phylogeny and historical biogeography of the swallow family (Hirundinidae) inferred from comparisons of thousands of UCE loci

Swallows (Hirundinidae) are a globally distributed family of passerine birds that exhibit remarkable similarity in body shape but tremendous variation in plumage, sociality, nesting behavior, and migratory strategies. As a result, swallow species have become models for empirical behavioral ecology and evolutionary studies, and variation across the Hirundinidae presents an excellent opportunity for comparative analyses of trait evolution. Exploiting this potential requires a comprehensive and well-resolved phylogenetic tree of the family. To address this need, we estimated swallow phylogeny using genetic data from thousands of ultraconserved element (UCE) loci sampled from nearly all recognized swallow species. Maximum likelihood, coalescent-based, and Bayesian approaches yielded a well-resolved phylogenetic tree to the generic level, with minor disagreement among inferences at the species level, which likely reflect ongoing population genetic processes. The UCE data were particularly useful in helping to resolve deep nodes, which previously confounded phylogenetic reconstruction efforts. Divergence time estimates from the improved swallow tree support a Miocene origin of the family, roughly 13 million years ago, with subsequent diversification of major groups in the late Miocene and Pliocene. Our estimates of historical biogeography support the hypothesis that swallows originated in the Afrotropics and have subsequently expanded across the globe, with major in situ diversification in Africa and a secondary major radiation following colonization of the Neotropics. Initial examination of nesting and sociality indicates that the origin of mud nesting – a relatively rare nest construction phenotype in birds – was a major innovation coincident with the origin of a clade giving rise to over 40% of extant swallow diversity. In contrast, transitions between social and solitary nesting appear less important for explaining patterns of diversification among swallows.

Five new unexpected populations of endangered tuco-tuco Ctenomys rionegrensis (Rodentia, Ctenomyidae) help understanding its distribution and historical biogeography

In this study, we conducted a survey of newly discovered populations of tuco-tuco (subterranean rodents of the genus Ctenomys) in the Entre Ríos province, in an area characterized by its unexplored nature and its climatic and biogeographic complexity within Argentina, which includes two National Parks. We characterize the nucleotide sequences of the cytochrome-b gene, revealing the presence of seven novel haplotypes within Ctenomys rionegrensis, a species known to inhabit both sides of the Uruguay River. Through Bayesian analyses, we estimated the divergence times of the oldest lineages of C. rionegrensis, as well as those of the haplotypes located east of the Uruguay River, dating back approximately 630,000 years before present (ybp) and 526,000 ybp, respectively. These estimates correspond with significant paleogeographic events in the region. Our findings may raise questions regarding the taxonomic classification of the species and suggest potential modifications to its current endangered status as designated by the International Union for Conservation of Nature (IUCN). Consequently, this research provides valuable insights that may inform future revisions of the species' conservation status and guide the development of informed management strategies/policies.

Phylogeny, character evolution and historical biogeography of Scurrulinae (Loranthaceae): new insights into the circumscription of the genus Taxillus

BackgroundExploring the relationship between parasitic plants and answering taxonomic questions is still challenging. The subtribe Scurrulinae (Loranthaceae), which has a wide distribution in Asia and Africa, provides an excellent example to illuminate this scenario. Using a comprehensive taxon sampling of the subtribe, this study focuses on infer the phylogenetic relationships within Scurrulinae, investigate the phylogeny and biogeography of the subtribe, and establish a phylogenetically-based classification incorporating both molecular and morphological evidence. We conducted phylogenetic, historical biogeography, and ancestral character state reconstruction analyses of Scurrulinae based on the sequences of six DNA regions from 89 individuals to represent all five tribes of the Loranthaceae and the dataset from eleven morphological characters.ResultsThe results strongly support the non-monophyletic of Scurrulinae, with Phyllodesmis recognized as a separate genus from its allies Taxillus and Scurrula based on the results from molecular data and morphological character reconstruction. The mistletoe Scurrulinae originated in Asia during the Oligocene. Scurrulinae was inferred to have been widespread in Asia but did not disperse to other areas. The African species of Taxillus, T. wiensii, was confirmed to have originated in Africa from African Loranthaceae ca. 17 Ma, and evolved independently from Asian members of Taxillus.ConclusionsThis study based on comprehensive taxon sampling of the subtribe Scurrulinae, strongly supports the relationship between genera. The taxonomic treatment for Phyllodesmis was provided. The historical biogeography of mistletoe Scurrulinae was determined with origin in Asia during the Oligocene. Taxillus and Scurrula diverged during the climatic optimum in the middle Miocene. Taxillus wiensii originated in Africa from African Loranthaceae, and is an independent lineage from the Asian species of Taxillus. Diversification of Scurrulinae and the development of endemic species in Asia may have been supported by the fast-changing climate, including cooling, drying, and the progressive uplift of the high mountains in central Asia, especially during the late Pliocene and Pleistocene.

Historical climate change and vicariance events contributed to the intercontinental disjunct distribution pattern of ash species (Fraxinus, Oleaceae)

The Northern Hemisphere temperate forests exhibit a disjunct distributional pattern in Europe, North America, and East Asia. Here, to reveal the promoter of intercontinental disjunct distribution, Fraxinus was used as a model organism to integrate abundant fossil evidence with high-resolution phylogenies in a phytogeographic analysis. We constructed a robust phylogenetic tree using genomic data, reconstructed the geographic ancestral areas, and evaluated the effect of incorporating fossil information on the reconstructed biogeographic history. The phylogenetic relationships of Fraxinus were highly resolved and divided into seven clades. Fraxinus originated in western North America during Eocene, and six intercontinental dispersal events and five intercontinental vicariance events were occured. Results suggest that climate change and vicariance contributed to the intercontinental disjunct distribution pattern of Fraxinus. Moreover, results highlight the necessity of integrating phylogenetic relationship and fossil to improve the reliability of inferred biogeographic events and our understanding of the processes underlying disjunct distributions.

Phylogeny and biogeography of harmochirine jumping spiders (Araneae: Salticidae)

We use ultraconserved elements (UCE) and Sanger data to study the phylogeny, age, and biogeographical history of harmochirine jumping spiders, a group that includes the species-rich genus Habronattus, whose remarkable courtship has made it the focus of studies of behaviour, sexual selection, and diversification. We recovered 1947 UCE loci from 43 harmochirine taxa and 4 outgroups, yielding a core dataset of 193 UCEs with at least 50 % occupancy. Concatenated likelihood and ASTRAL analyses confirmed the separation of harmochirines into two major clades, here designated the infratribes Harmochirita and Pellenita. Most are African or Eurasian with the notable exception of a clade of pellenites containing Habronattus and Pellenattus of the Americas and Havaika and Hivanua of the Pacific Islands. Biogeographical analysis using the DEC model favours a dispersal of the clade’s ancestor from Eurasia to the Americas, from which Havaika’s ancestor dispersed to Hawaii and Hivanua’s ancestor to the Marquesas Islands. Divergence time analysis on 32 loci with 85 % occupancy, calibrated by fossils and island age, dates the dispersal to the Americas at approximately 4 to 6 million years ago. The explosive radiation of Habronattus perhaps began only about 4 mya. The phylogeny clarifies both the evolution of sexual traits (e.g., the terminal apophyses was enlarged in Pellenes and not subsequently lost) and the taxonomy. Habronattus is confirmed as monophyletic. Pellenattus is raised to the status of genus, and 13 species moved into it as new combinations. Bianor stepposus Logunov, 1991 is transferred to Sibianor, and Pellenes bulawayoensis Wesołowska, 1999 is transferred to Neaetha. A molecular clock rate estimate for spider UCEs is presented and its utility to inform prior distributions is discussed.