Complex Biogeographic History Research Articles

Fossil-informed biogeographic analysis suggests Eurasian regionalization in crown Squamata during the early Jurassic.

Squamata (lizards, snakes, and amphisbaenians) is a Triassic lineage with an extensive and complex biogeographic history, yet no large-scale study has reconstructed the ancestral range of early squamate lineages. The fossil record indicates a broadly Pangaean distribution by the end- Cretaceous, though many lineages (e.g., Paramacellodidae, Mosasauria, Polyglyphanodontia) subsequently went extinct. Thus, the origin and occupancy of extant radiations is unclear and may have been localized within Pangaea to specific plates, with potential regionalization to distinct Laurasian and Gondwanan landmasses during the Mesozoic in some groups. We used recent tectonic models to code extant and fossil squamate distributions occurring on nine discrete plates for 9,755 species, with Jurassic and Cretaceous fossil constraints from three extinct lineages. We modeled ancestral ranges for crown Squamata from an extant-only molecular phylogeny using a suite of biogeographic models accommodating different evolutionary processes and fossil-based node constraints from known Jurassic and Cretaceous localities. We hypothesized that the best-fit models would not support a full Pangaean distribution (i.e., including all areas) for the origin of crown Squamata, but would instead show regionalization to specific areas within the fragmenting supercontinent, likely in the Northern Hemisphere where most early squamate fossils have been found. Incorporating fossil data reconstructs a localized origin within Pangaea, with early regionalization of extant lineages to Eurasia and Laurasia, while Gondwanan regionalization did not occur until the middle Cretaceous for Alethinophidia, Scolecophidia, and some crown Gekkotan lineages. While the Mesozoic history of extant squamate biogeography can be summarized as a Eurasian origin with dispersal out of Laurasia into Gondwana, their Cenozoic history is complex with multiple events (including secondary and tertiary recolonizations) in several directions. As noted by previous authors, squamates have likely utilized over-land range expansion, land-bridge colonization, and trans-oceanic dispersal. Tropical Gondwana and Eurasia hold more ancient lineages than the Holarctic (Rhineuridae being a major exception), and some asymmetries in colonization (e.g., to North America from Eurasia during the Cenozoic through Beringia) deserve additional study. Future studies that incorporate fossil branches, rather than as node constraints, into the reconstruction can be used to explore this history further.

Molecular variation and phylogeography within European Isothecium alopecuroides and Pseudisothecium myosuroides (Bryophyta, Lembophyllaceae)

Abstract Earlier studies on Isothecium s.l. suggested potential interchange of genetic material between species that are nowadays known to belong to separate genera. In this study, we analyse the variation in three molecular markers (nuclear gpd; mitochondrial nad5; and plastid trnG) in a wide selection of Isothecium alopecuroides and Pseudisothecium myosuroides specimens to infer whether this potential exchange of genetic material is frequent. In addition, we explore the phylogeographic structure of these two species in Europe. Our results seem to show repeated genetic interchange for the nuclear and mitochondrial markers in both species, suggesting intergeneric hybridization, although horizontal gene transfer and/or incomplete lineage sorting could also explain the detected incongruences. The genetic lineages found indicate a complex biogeographical history for I. alopecuroides, including both post-glacial immigration from different glacial refugia and developing haplotypes potentially adapted to cold climates. As for P. myosuroides, genetic variants could either indicate a post-glacial immigration history or adaptation to oceanic conditions. Further studies including a larger set of more variable molecular markers could help to reach final conclusions on the results here presented.

The role of ecological niche conservatism in the evolution of bird distributional patterns in Mesoamerican seasonally dry forests

AbstractAimDue to its complex biogeographical and ecological history, the seasonally dry forests (SDF) of Mesoamerica are considered a biodiversity hotspot. SDF are currently distributed in relatively large and continuous, but isolated areas, in which there are both high total and endemic species numbers. Among birds, few species are shared across SDF patches; other species are endemic to one of these; and for two species currently endemic to one patch, fossils have been recovered in a different one, suggesting a former widespread distribution in so species, implying that current distributional patterns are probably recent.LocationMesoamerican seasonally dry forests.MethodsWe assessed the role of niche divergence/conservatism in the evolution of bird distributional patterns. Using an ecological niche modelling approach, we estimated palaeodistributions for two species currently endemic to the SDF of Yucatan Peninsula (YP), two to the Mesoamerican Pacific Slope (MPS) with fossil record in the YP and two more showing an allopatric pattern. For comparison, we simulated virtual species (VS) matching each pattern, assuming they represent the expected distribution of species in each SDF patch. To test hypothesis of niche conservatism, we assessed the niche equivalence/similarity between the patches represented by the VS, and in each bird species and its VS distributional counterpart.ResultsOur results showed three patterns: (i) no past geographical connectiveness among suitable areas; (ii) niche conservatism, but not equivalence, despite low niche overlap and geographical distance; and (iii) potential niche divergence.Main ConclusionsFor birds currently endemic to the MPS, our results suggest that the absence from the YP may be attributed to the loss of their environmental niche. Widespread species showed either niche conservatism or divergence. YP endemics showed niche divergence. Our results underline the role of niche divergence/conservatism in the evolution of distributional patterns in Mesoamerican SDF avifauna.

Discovery of a new tarantula species from the Madrean Sky Islands and the first documented instance of syntopy between two montane endemics (Araneae, Theraphosidae, Aphonopelma): a case of prior mistaken identity.

The Chiricahua Mountains in southeastern Arizona are renowned for their exceptional biodiversity and high levels of endemism. Morphological, genomic, behavioral, and distributional data were used to report the discovery of a remarkable new tarantula species from this range. Aphonopelmajacobii sp. nov. inhabits high-elevation mixed conifer forests in these mountains, but also co-occurs and shares its breeding period with A.chiricahua-a related member of the Marxi species group-in mid-elevation Madrean evergreen oak and pine-oak woodlands. This marks the first documented case of syntopy between two montane endemics in the Madrean Archipelago and adds to our knowledge of this threatened region's unmatched tarantula diversity in the United States. An emended diagnosis and redescription for A.chiricahua are also provided based on several newly acquired and accurately identified specimens. Phylogenetic analyses of mitochondrial and genomic-scale data reveal that A.jacobii sp. nov. is more closely related to A.marxi, a species primarily distributed on the Colorado Plateau, than to A.chiricahua or the other Madrean Sky Island taxa. These data provide the evolutionary framework for better understanding the region's complex biogeographic history (e.g., biotic assembly of the Chiricahua Mountains) and conservation of these spiders.

Fishes of the upper rio Paraná basin: diversity, biogeography and conservation

Abstract The upper rio Paraná basin drains the most developed and environmentally degraded region in South America: the Brazilian southeast. While it is one of the most well-known Neotropical fish assemblages, it is also one of the most threatened by anthropic activity. Urbanization, deforestation, dam construction, invasive species, and water pollution not only reduce the living area of species but also alter our perception of the basin and its biotic elements. Such changes are so profound and pervasive that raise uncertainties about the native or non-native status of several species. This paper aims to offer a detailed picture of the native diversity and historical biogeography of the fishes in the upper rio Paraná basin, which we hope will offer a solid foundation for future conservation policies. We update the list of native species, analyze geographical distributions, and identify biogeographical patterns, emphasizing areas requiring recognition as distinct biotas for conservation efforts. Over the past 15 years, more than 100 additional species have been described or recorded, expanding the total to 341 native species belonging to six orders and 30 families, making it the richest river basin in Brazil outside the Amazonian region. Unlike most neotropical basins where Characidae dominates, loricariids make up nearly one-fourth of the total fish diversity in the region. Species and clades concentrate in the central basin, while endemics are confined to peripheral areas due to the complex biogeographical history shared with neighboring basins. Eighteen distinct biogeographical regions are identified, discussing their composition, histories, and conservation implications. The upper rio Paraná basin has 10% of its fish fauna ranked as endangered and present 128 non-native species, including three hybrids. This places it as the major drainage with the largest number of endangered taxa in the neotropics and at the same time the one with the most numerous non-native elements. Existing protected areas are deemed ineffective in preserving diverse assemblages and fail to safeguard the majority of threatened and narrowly-endemic species.

Unraveling the complex phylogeographic history of freshwater fishes in Lower Central America: A study of the electric fish Brachyhypopomus occidentalis

Lower Central America (LCA) has a complex biogeographic history shaped by the rise of the Isthmus of Panama and the global climatic oscillations of the Pleistocene. These events have been crucial in structuring biodiversity in LCA, but their consequences for the distribution and partitions of genetic diversity across the region remain to be elucidated. We combined complete mitochondrial genomes and nuclear ultraconserved elements (UCEs) to study the phylogeographic history and population genetic structure of the electric fish Brachyhypopomus occidentalis in LCA. Our results are consistent with the known phylogeographic history of B. occidentalis in LCA, but we update this history in several important ways that help illuminate the phylogeographic history of freshwater fishes in the region. We provide: i) support for three waves of colonization, two of which occurred prior to the final closure of the Panama Isthmus; ii) a more precise understanding of each colonization event, with evidence for a larger footprint of the first event, as well as genetic exchange across the continental divide in subsequent events; and iii) evidence for high levels of previously unrecognized population genetic structure across LCA. This updated model of colonization and diversification of B. occidentalis consists of three waves of dispersal and colonization, which triggered the evolution of geographic breaks in both nuclear and mitochondrial genomes across LCA. These processes are tightly linked to the dynamic uplift of the Isthmus, recent volcanic activity in the region, and the sea-level oscillations of the Pleistocene. These results improve previous phylogeographic inferences regarding the distribution and diversification of freshwater fishes in LCA, and generate testable hypotheses to guide future research exploring the factors shaping biodiversity in the region.

From southern Africa and beyond: Historical biogeography of a monocotyledonous bulbous geophyte

AbstractAimLow taxon sampling and taxonomic uncertainties still obscure our evolutionary knowledge of many taxa, especially widespread lineages across diverse landscapes. Of particular interest are those lineages inhabiting seasonal and arid landscapes, which showcase unique distributional patterns that hint at fascinating histories. Using the most comprehensive sampling to date of a widespread bulbous monocot, we hypothesize two independent dispersals to Madagascar, and that vicariance due to Miocene‐driven aridification contracted a once‐widespread distribution between Africa and Eurasia.LocationSub‐Saharan Africa, Madagascar, Eurasia.TaxonLedebouriinae (Scilloideae, Asparagaceae).MethodsUsing the Angiosperms353 probe set for 195 taxa (86 ingroup taxa), we perform phylogenetic reconstruction using IQ‐Tree, and we infer age estimates using penalized likelihood as implemented in treePL. Capitalizing on our broad geographic sampling, which includes African, Malagasy and Eurasian taxa, we use ‘BioGeoBEARS’ to reconstruct ancestral ranges and investigate the role of vicariance and dispersal.ResultsThe Ledebouriinae originated within the past c. 30 myr in south‐eastern sub‐Saharan Africa, with the major subclades arising soon thereafter. Although long‐distance dispersal cannot be fully ruled out, we argue that vicariance was the major process responsible for the current distribution of Ledebouria in Eurasia. We recover two distinct Ledebouria groups that overlap in eastern Africa but are divided into mostly northern and southern clades with divergent biogeographical histories, each showing an independent dispersal to Madagascar. A similar north–south split is seen in Drimiopsis. Additionally, we recover a complex biogeographic history in the predominantly sub‐Saharan African Ledebouria clade, with rapid radiation at c. 14 mya.Main ConclusionsThe expansion of seasonal rainfall and aridity in sub‐Saharan Africa, coupled with orogenic activity, may have fostered the diversification of the Ledebouriinae and many subclades. Miocene‐driven aridification may have caused fragmentation of a once widespread distribution that led to their occurrence in Eurasia.

The ichthyofaunistic colonization and complex biogeographic history of the southern portion of the Southwest Atlantic Ocean

AbstractHere, we highlight the geological processes that resulted in the current conformation of the southern Southwest Atlantic Ocean, and explore the heterogeneous composition of the marine ichthyofauna found between 33° and 56° from a paleobiological perspective. During the early Cretaceous (140 Mya), the South Atlantic was still not formed, and Gondwana was probably a set of united plates with shallow continental waters. In the middle Cretaceous (112 Mya), the major Gondwanan plates started diverging from each other, allowing shallow marine intrusions and the diversification of an endemic fish fauna. By the end of the Mesozoic (66 Mya), the proto‐South Atlantic connected with the North Atlantic, which was still part of the Tethys Sea, allowing its ichthyofauna to colonize the south and reach the Antarctic region. The opening of the Drake Passage in the Oligocene (33 Mya) enabled the cold waters of the Pacific Ocean to reach the South Atlantic, causing drastic effects on the thermophilic fauna and favoring the dispersion of cold‐water species. Successive glaciations during the Quaternary (2 Myr to 10,000 years ago) resulted in the prevalence of Antarctic climatic conditions in the southern Southwest Atlantic. The long history of changing scenarios in the constitution of the southern Southwest Atlantic is reflected in the heterogeneous composition of the marine ichthyofauna between 33° and 56°S, which is characterized by a mixture of cosmopolitan, Tethyan, Pacific, Gondwanan, Antarctic, and endemic origins.

In the land of the blind: Exceptional subterranean speciation of cryptic troglobitic spiders of the genus Tegenaria (Araneae: Agelenidae) in Israel

Caves have long been recognized as a window into the mechanisms of diversification and convergent evolution, due to the unique conditions of isolation and life in the dark. These lead to adaptations and reduce dispersal and gene flow, resulting in high levels of speciation and endemism. The Israeli cave arachnofauna remains poorly known, but likely represents a rich assemblage. In a recent survey, we found troglophilic funnel-web spiders of the genus Tegenaria in 26 caves, present mostly at the cave entrance ecological zone. In addition, we identified at least 14 caves inhabited by troglobitic Tegenaria, which are present mostly in the twilight and dark ecological zones. Ten of the caves, located in the north and center of Israel, are inhabited by both troglophilic and troglobitic Tegenaria. These spiders bear superficial phenotypic similarities but differ in the levels of eye reduction and pigmentation. To test whether these taxa constitute separate species, as well as understand their relationships to epigean counterparts, we conducted a broad geographic sampling of cave-dwelling Tegenaria in Israel and Palestine, using morphological and molecular evidence. Counterintuitively, our results show that the troglobitic Tegenaria we studied are distantly related to the troglophilic Tegenaria found at each of the cave entrances we sampled. Moreover, seven new troglobitic species can be identified based on genetic differences, eye reduction level, and features of the female and male genitalia. Our COI analysis suggest that the Israeli troglobitic Tegenaria species are more closely related to eastern-Mediterranean congeners than to the local sympatric troglophile Tegenaria species, suggesting a complex biogeographic history.

Biogeographic patterns of hydrozoans in the Gulf of Mexico and adjacent waters: biological assemblages, beta diversity, and endemism

The biogeography of hydrozoans encompasses a broad scope of study that involves various challenges due to their diverse distributional strategies and life cycle characteristics. This work aims to study the biogeographic patterns of hydrozoans in the Gulf of Mexico. Occurrence records on hydrozoans were compiled through the Global Biodiversity Facility Information database and peer-reviewed literature. Biogeographic patterns were addressed through (1) the identification of biological assemblages, using hierarchical clustering with contiguity constraint; (2) the decomposition of beta diversity into species replacement, nestedness, and local contribution to beta diversity (LCBD); and (3) the identification of areas of endemism with a parsimony analysis of endemicity (PAE). The northern Gulf of Mexico and the Yucatán Peninsula contain a large hydrozoan assemblage that splits into smaller groups at different levels, characterized by species replacement and high LCBD values. By contrast, the southern Gulf of Mexico contains a homogenous assemblage, which exhibits low LCBD values and contributes strongly to nestedness. PAE identified 19 areas of higher-level endemism, concentrated mainly in shelf zones of the Yucatán and Florida peninsulas. The distribution patterns of hydrozoans in the Gulf of Mexico may be shaped by the life cycle characteristics of the taxa and the geological history of the region, relating either to neritic or oceanic zones. The northern Gulf reflects a heterogeneous biological composition with a complex biogeographical history, which makes this area of particular interest for future studies, as it likely represents a transition zone. This premise must be corroborated in the future.

Phylogenomics Reveals that Mitochondrial Capture and Nuclear Introgression Characterize Skua Species Proposed to be of Hybrid Origin.

The skuas and jaegers (Stercorariidae) are an enigmatic family of seven seabird species that breed at Arctic and Antarctic latitudes. The phylogenetic relationships amongst the species have been controversial, with one of the biggest enigmas involving the Pomarine Jaeger (Stercorarius pomarinus), which has been proposed to represent a hybrid species originating from the merging of distant lineages within the complex. We inferred a phylogeny for the family using multispecies coalescent methods with whole-genome sequencing for all seven species of Stercorariidae, and document an evolutionary history rich in introgression. We uncover evidence for mitochondrial capture and nuclear introgression between S. pomarinus and Stercorarius skua, providing a potential avenue for adaptive introgression. One candidate for adaptive introgression is the MC1R plumage gene which appears to have introgressed from one of the large skuas into S. pomarinus, where it now forms the basis of the dark-morph color polymorphism of that species. We further highlight a complex biogeographical history of interchange between the Arctic and Antarctic, with unexpected close ancestry between S. skua of the northern hemisphere and Stercorarius antarcticus of the southern hemisphere. These results highlight the dynamic history of introgression during pelagic seabird radiation. [Incomplete lineage sorting; introgression; mitochondrial capture; phylogenomics; skua; species tree; stercorariidae; whole-genome resequencing.].

Mitochondrial DNA sequences and nuclear microsatellites reveal population genetic structure of the range-restricted hummingbird Phaeoptila sordida in the Balsas Basin

Abstract The Dusky Hummingbird Phaeoptila sordida (= Cynanthus sordidus), occurs in the Balsas Basin, a region with a complex biogeographical history, and in the Tehuacán-Cuicatlán Valley and Valles Centrales in Puebla and Oaxaca, Mexico. However, the biogeographical and evolutionary history of these two regions of Mexico is poorly understood. We aimed to understand the genetic structure and phylogeographic history of P. sordida, a range-restricted hummingbird to these two regions, as a proxy to study the evolutionary history of the Balsas Basin, by using mitochondrial DNA (mtDNA) sequences and nuclear microsatellites. Geographic structure was evident for both markers; however, some discordance was observed between the mitochondrial and nuclear markers. Based on mtDNA, samples from the Balsas Basin form one haplogroup, well separated from the Tehuacán-Cuicatlán Valley and Valles Centrales samples. In contrast to this, nuclear microsatellites uncovered two slightly different genetic clusters restricted to different habitats: samples from the Western Balsas restricted to the seasonally deciduous tropical dry forest, and samples from the Eastern Balsas-Tehuacán/Cuicatlán-Tehuantepec area in shrub and dry forested habitats. As expected by the interglacial refugia hypothesis, ENM predicted that the distribution of P. sordida was more contracted and fragmented during the Last Inter Glacial and more expanded at the Last Glacial Maximum. Consistent with that observed for other range-restricted hummingbird species, ENM predictions and a strong signal of population expansion indicate that the geographical range and population size are unstable over time, as compared to widespread hummingbird species, and that ecological and climatic factors possibly impacted its diversification. This study contributes to the debate that disputes the integrity of the Balsas Basin as a biogeographical unit and urges for the conservation of endemic species in the Balsas region and interior Oaxaca.

Genomic divergence, local adaptation, and complex demographic history may inform management of a popular sportfish species complex.

The Neosho Bass (Micropterus velox), a former subspecies of the keystone top‐predator and globally popular Smallmouth Bass (M. dolomieu), is endemic and narrowly restricted to small, clear streams of the Arkansas River Basin in the Central Interior Highlands (CIH) ecoregion, USA. Previous studies have detected some morphological, genetic, and genomic differentiation between the Neosho and Smallmouth Basses; however, the extent of neutral and adaptive divergence and patterns of intraspecific diversity are poorly understood. Furthermore, lineage diversification has likely been impacted by gene flow in some Neosho populations, which may be due to a combination of natural biogeographic processes and anthropogenic introductions. We assessed: (1) lineage divergence, (2) local directional selection (adaptive divergence), and (3) demographic history among Smallmouth Bass populations in the CIH using population genomic analyses of 50,828 single‐nucleotide polymorphisms (SNPs) obtained through ddRAD‐seq. Neosho and Smallmouth Bass formed monophyletic clades with 100% bootstrap support. We identified two major lineages within each species. We discovered six Neosho Bass populations (two nonadmixed and four admixed) and three nonadmixed Smallmouth Bass populations. We detected 29 SNPs putatively under directional selection in the Neosho range, suggesting populations may be locally adapted. Two populations were admixed via recent asymmetric secondary contact, perhaps after anthropogenic introduction. Two other populations were likely admixed via combinations of ancient and recent processes. These species comprise independently evolving lineages, some having experienced historical and natural admixture. These results may be critical for management of Neosho Bass as a distinct species and may aid in the conservation of other species with complex biogeographic histories.

The evolutionary history of the relict scorpion family Iuridae of the eastern Mediterranean

Iuridae is a family of scorpions that exhibits a highly complex biogeographic and taxonomic history. Iuridae taxa are mainly found in Turkey and Greece, whereas a single species is found in northern Iraq. Several taxonomic revisions have been conducted on this family that initially comprised two genera. The latest taxonomic review, based on morphological and anatomical features, raised the number of Iuridae genera to four, and the number of species to 14.Sequence data from three molecular markers (COX1, 16S rDNA, ITS1) originating from numerous Iuridae taxa were analyzed within a phylogenetic framework. Divergence time-estimate analyses, species delimitation approaches and estimation of ancestral areas were implemented in order to: (1) reconstruct the phylogenetic relationships of the Iuridae taxa, (2) evaluate the morphological classifications, and (3) obtain insights into the biogeographic history of the family in the East Mediterranean.The multi-locus phylogeny clearly confirms an ancient division into two clades, Calchinae and Iurinae. Ancient patterns of isolation and dispersal are revealed. Both subfamilies are largely confined to the Anatolian peninsula and its few coastal islands; only the most derived genus Iurus has dispersed westward to Crete and Peloponnese. Based on our findings, three new genera of Iurinae (Metaiurus, Anatoliurus, and Letoiurus) are established. The genus Neocalchas emerges as one of the most ancient scorpion clades, with divergence time about 27 mya.

A new ornithopod dinosaur, Transylvanosaurus platycephalus gen. et sp. nov. (Dinosauria: Ornithischia), from the Upper Cretaceous of the Haţeg Basin, Romania

ABSTRACT Rhabdodontid dinosaurs were a group of medium-sized iguanodontian ornithopods from the Late Cretaceous of Europe. The uppermost Cretaceous continental deposits from the Haţeg Basin of western Romania yielded a very rich assemblage of vertebrates including abundant rhabdodontid remains, which have been exclusively referred to the genus Zalmoxes thus far. Here we describe a new rhabdodontid dinosaur, Transylvanosaurus platycephalus gen. et sp. nov., from the uppermost Cretaceous of the Haţeg Basin. The holotype of the new taxon was discovered in early–late Maastrichtian strata near Pui in the eastern part of the basin and comprises the articulated basicranium and both frontals. Transylvanosaurus differs from all previously reported rhabdodontids in having particularly wide and crested frontals, elongated and straight paroccipital processes that make only a gentle lateral curve and project mostly posterolaterally, prominent and massive prootic processes that extend mainly anterolaterally and ventrally, wide and crest-like basal tubera that meet the long axis of the braincase at a very flat angle, widely splayed basipterygoid processes that extend mainly ventrolaterally and slightly anteriorly, as well as a well-developed notch on the lateral side of the basicranium that is continuous, straight, and inclined anteroventrally. Phylogenetic analyses employing two different datasets consistently recovered the new taxon within the Rhabdodontidae, at the base of the iguanodontian radiation. Based on the morphological comparisons presented herein, we propose a particularly close relationship between Transylvanosaurus and Rhabdodon from southern France, which in turn provides evidence for a more complex biogeographic history of the Rhabdodontidae than previously thought.

Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere.

Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian-western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.

Species limits and recent diversification of Cerradomys (Sigmodontinae: Oryzomyini) during the Pleistocene.

Cerradomys is a genus of the tribe Oryzomyini with eight species currently recognized, and a controversial taxonomy. These species are mainly distributed in the South America dry diagonal, but some species extend into Atlantic Forest, reaching the coastal sandy plains known as Restingas. This study aimed to address species limits and patterns of diversification of Cerradomys species. For this purpose, we performed cytogenetic and molecular analyses (phylogeny, coalescent species delimitation, barcoding, and divergence times estimation) using multiple mitochondrial and nuclear markers on a comprehensive sampling, representing all nominal taxa reported so far. Chromosomal information was a robust marker recognizing eight Cerradomys species. Reciprocal monophyly was recovered for all the species, except for C. subflavus. These results together with coalescent analyses recovered eight species as the most congruent species delimitation scenario for the genus (mean Ctax: 0.72). Divergence time estimates revealed that Cerradomys’ diversification occurred about 1.32 million years ago (Mya) during the Pleistocene. Although our results conservatively support the eight Cerradomys species described so far, different lines of evidence suggest that C. langguthi and C. subflavus could potentially be species-complexes. We discussed this scenario in the light of multiple evolutionary processes within and between species and populations, since Cerradomys comprises a species group with recent diversification affected by Pleistocene climatic changes and by the complex biogeographic history of South America dry diagonal. This work supports that the diversity of Cerradomys is underestimated and reiterates that interdisciplinary approaches are mandatory to identify small rodent species properly, and to unhide cryptic species.

Role of the Andean uplift as an asymmetrical barrier to gene flow in the neotropical leaf‐cutting ant Atta cephalotes

AbstractNeotropical diversification by the Andean uplift is typically addressed on a large evolutionary scale (e.g., speciation), even though many species are still distributed in both sides of the mountains. The three parallel mountain ranges in the northern Andes (Colombia) impose a major geographical barrier to species’ migration from South to Central America. How important these barriers are for conspecific diversification of cross‐Andean species such as the leaf‐cutting ants remains largely unknown. To answer this question, we studied the mtCOI gene of Atta cephalotes, the most widely distributed leaf‐cutting ant species. Our hierarchical analyses evidenced substantial genetic structure among regions and populations, suggesting a more complex biogeographical history of Andean populations than previously thought. These mountains seem to isolate Central American and Western Colombian populations from the rest of A. cephalotes in South America. Population and migration modeling are consistent with the origin of this species in South America and a major role of the Eastern cordillera as a geographical barrier to historical gene flow, restricting dispersion from north to south. These findings provide insights into the role of the Andean uplift as barrier to gene flow in species of leaf‐cutting ants.Abstract in Spanish is available with online material.

Cretaceous mammals of India–Stratigraphic distribution, diversity and intercontinental affinities

Extensive research carried out on the Cretaceous deposits of Laurasia has revealed an overwhelming presence of eutherian, metatherian and multituberculate groups of mammals in the Cretaceous ecosystems of Northern Hemisphere continents. In contrast, the relatively poorly documented fossil record of Cretaceous mammals from Gondwanan continents is represented by gondwanatherians, dryolestoids, and a few multituberculates and haramiyidans. Until now, no undoubted eutherian mammals have been reported from the Cretaceous strata of the southern continents except for India. In this context, Indian Cretaceous mammals assume great significance for understanding the origin and evolution of these mammals in Gondwana. Currently, the Cretaceous mammals of India include three groups, viz., eutherians, gondwanatherians, and haramiyidans. These three mammalian groups were recovered primarily from the Upper Cretaceous Deccan infra–and inter–trappean beds of peninsular India exposed near Bacharam, Naskal and Rangapur (Telengana), Upparhatti (Karnataka) and Kisalpuri (Madhya Pradesh) villages. Eutheria is by far the most diverse clade comprising three named genera (Deccanolestes, Sahnitherium, Kharmerungulatum) and one unnamed taxon (Eutheria incertae sedis). The gondwanatherians are known by Bharattherium bonapartei and Sudamericidae gen. et sp. indet. The third mammalian group, a possible haramiyidan, is represented by a solitary species Avashishta bacharamensis. Overall, the Cretaceous mammal fauna of India presents a complex biogeographic history with eutherians of Laurasian affinity, pan–Gondwanan gondwanatherians and a possible late surviving haramiyidan. Numerically abundant and speciose Deccanolestes, identified as an adapisoriculid, has been interpreted to have had originated in northward drifting Indian Plate in the Late Cretaceous and dispersed out of India into Africa and Europe over island arc systems (Oman–Kohistan–Dras) and the Ladakh magmatic arc at or near the Cretaceous–Paleogene boundary. A similar dispersal mode has also been visualized for Kharmerungulatum and Eutheria incertae sedis of Laurasian affinities. The close similarity of dental morphology between Madagascan and Indian gondwanatherians attests to the fact that these taxa derived from a common endemic Gondwanan stock had evolved in isolation following the separation of Indo–Madagascar from other Gondwanan continents. Avashishta represents a late Gondwana survivor of a group that had a Pangaean distribution until the Early Cretaceous.

Exploring the effects of the quaternary glacial–interglacial cycles on the geographic distributions of tropical Andean rodents: species in the genus Aepeomys Thomas, 1898 (Thomasomyini: Sigmodontinae: Cricetidae) as a case study

ABSTRACT The Quaternary glaciations had great impacts on the historical biogeography of small mammal species. Recent studies have showed the effects of these climatic cycles on the diversification of several Neotropical rodents, but these have focused on species whose distributions do not encompass the tropical Andes. Thus, the influences of these climatic dynamics on the evolutionary history of tropical Andean rodent species remain unknown. The effects of these climatic changes were addressed on Aepeomys lugens and A. reigi, two Thomasomyine endemics from the Cordillera de Mérida in the Venezuelan Andes. The past potential geographic distribution of both species was inferred using an ecological niche modeling approach. The estimations obtained indicated that the availability of the suitable climatic conditions for these taxa has varied in size and location during the last 140,000 years. The spatial projection of the niche models onto the climatic scenarios explored indicates that the effects over the historical distributions were smaller in A. lugens than in A. reigi. These results show that the current geographic distribution of both Andean rodents conceals complex biogeographic histories, and characterizations of the demographic history and genetic diversity will be required to understand the evolution of the genus Aepeomys in the Andes.