Biogeographic Reconstructions Research Articles

Standing on the shoulders of giants: molecular data confirm Kükenthal’s systematic placement of the Australian endemic Carex archeri (Cyperaceae)

Archer’s sedge (Carex archeri Boott) is a small, rare (or possibly overlooked by collectors due to the diminutive size) species restricted to alpine and subalpine habitats in south-eastern mainland Australia and Tasmania. The systematic placement has been obscure with the species having been historically associated with sections in four of the six recognised Carex subgenera. We investigated the placement of C. archeri by addition to the available Carex molecular phylogenetic framework. Our results support C. archeri belonging to sect. Junciformes (in subg. Psyllophorae), making this the only representative of the subgenus in Australia. This placement was first proposed by Kükenthal (1909) who regarded C. archeri as a synonym of the New Zealand endemic C. acicularis Boott but our phylogenetic analyses support C. archeri as a separate taxon. Our approach highlights the utility of molecular barcoding for elucidating systematic relationships of poorly known taxa. Biogeographic reconstruction suggests Late Miocene dispersal from South America to the south-western Pacific but does not clarify whether New Zealand or Australia was colonised first. We evaluate the conservation status of Carex archeri using IUCN criteria as Endangered at the global level. At the state level, we propose Critically Endangered status in New South Wales, Endangered in Victoria and Data Deficient in Tasmania.

Complete chloroplast genome sequence of Artemisia littoricola (Asteraceae) from Dokdo Island Korea: genome structure, phylogenetic analysis, and biogeography study.

The Asteraceae family, particularly the Artemisia genus, presents taxonomic challenges due to limited morphological characteristics and frequent natural hybridization. Molecular tools, such as chloroplast genome analysis, offer solutions for accurate species identification. In this study, we sequenced and annotated the chloroplast genome of Artemisia littoricola sourced from Dokdo Island, employing comparative analyses across six diverse Artemisia species. Our findings reveal conserved genome structures with variations in repeat sequences and junction boundaries. Notably, the chloroplast genome of A. littoricola spans 150,985bp, consistent with other Artemisia species, and comprises 131 genes, including 86 protein-coding, 37 tRNA, and 8 rRNA genes. Among these genes, 16 possess a single intron, while clpP and ycf3 exhibit two introns each. Furthermore, 18 genes display duplicated copies within the IR regions. Moreover, the genome possesses 42 Simple Sequence Repeats (SSRs), predominantly abundant in A/T content and located within intergenic spacer regions. The analysis of codon usage revealed that the codons for leucine were the most frequent, with a preference for ending with A/U. While the chloroplast genome exhibited conservation overall, non-coding regions showed lower conservation compared to coding regions, with the Inverted Repeat (IR) region displaying higher conservation than single-copy regions. Phylogenetic analyses position A. littoricola within subgenus Dracunculus, indicating a close relationship with A. scoparia and A. desertorum. Additionally, biogeographic reconstructions suggest ancestral origins in East Asia, emphasizing Mongolia, China (North East and North Central and South Central China), and Korea. This study underscores the importance of chloroplast genomics in understanding Artemisia diversity and evolution, offering valuable insights into taxonomy, evolutionary patterns, and biogeographic history. These findings not only enhance our understanding of Artemisia's intricate biology but also contribute to conservation efforts and facilitate the development of molecular markers for further research and applications in medicine and agriculture.

Investigation of the distribution patterns in moinids (Crustacea: Cladocera: Moinidae) forming ephippia with two resting eggs

During last two decades, morphological and genetic studies of the microcrustaceans from the family Moinidae Goulden, 1968 (Crustacea: Branchiopoda: Cladocera) were intensified. However, species diversity within this family remains underestimated. It refers to both subtropical and tropical areas of different continents that have traditionally been less studied compared with Central Europe and some other Palaearctic regions. In addition to this, only a restricted set of morphological characteristics is used for the discrimination of species within the genus Moina Baird, 1850. Most common moinid taxa are considered species complexes rather than single species, making any biogeographic reconstruction difficult. Here, we present an investigation of distribution patterns in moinids that form ephippia with two resting eggs based on both a reexamination of data from the literature and from specimens in museum and personal collections. Also, we redescribed morphology of poorly known taxa from the arid regions of the Old World—Moina belli Gurney, 1904 and M. kaszabi Forró, 1988 and clarify their diagnostic morphological characters and distributional ranges. We found that M. belli and M. kaszabi are morphologically very similar. In both species, setae 1 and 2 of thoracic limb I are armed bilaterally by fine, densely located short setulae. Reliable differences between M. belli and M. kaszabi concern armature of the valve posteroventral portion. Among the moinids with two resting eggs in the ephippium, M. belli and M. kaszabi are morphologically closer to M. macrocopa (Straus, 1820) and M. americana Goulden, 1968. All these species have: (1) a dorsal head pore; (2) fine long hairs on head, valve and preanal margin of postabdomen; (3) thoracic limb I of male with a long exopodite. In general, an investigated group of moinids includes both species with relatively compact and very broad distributional ranges. We concluded that maximum diversity of the moinids forming ephippia with two resting eggs is characteristic of southern portions of Palaearctic and Nearctic zoogeographical regions and approximately corresponds to subtropical climate zone. We need to underline that M. macrocopa and M. americana have a great invasive potential. Both species were anthropogenically introduced in South America and have been successfully naturalized there. Their distribution in tropical regions of the Old World and Australia requires new precise investigations. A group of moinids forming ephippia with two resting eggs can be considered as a convenient model for biogeographical reconstructions, including studies on changes in aquatic ecosystems due to global climate warming, eutrophication and the introduction of non-native species. There is no doubt that subsequent joint application of morphological and genetic data will shed more light on the global phylogeographic structure of the entire family Moinidae.

Accounting for extinction dynamics unifies the geological and biological histories of Indo-Australian Archipelago.

Biogeographical reconstructions of the Indo-Australian Archipelago (IAA) have suggested a recent spread across the Sunda and Sahul shelves of lineages with diverse origins, which appears to be congruent with a geological history of recent tectonic uplift in the region. However, this scenario is challenged by new geological evidence suggesting that the Sunda shelf was never submerged prior to the Pliocene, casting doubt on the interpretation of recent uplift and the correspondence of evidence from biogeography and geology. A mismatch between geological and biogeographical data may occur if analyses ignore the dynamics of extinct lineages, because this may add uncertainty to the timing and origin of clades in biogeographical reconstructions. We revisit the historical biogeography of multiple IAA taxa and explicitly allow for the possibility of lineage extinction. In contrast to models assuming zero extinction, we find that all of these clades, including plants, invertebrates and vertebrates, have a common and widespread geographic origin, and each has spread and colonized the region much earlier than previously thought. The results for the eight clades re-examined in this article suggest that they diversified and spread during the early Eocene, which helps to unify the geological and biological histories of IAA.

Phylogenetic relationships and historical biogeography of silkmoths (Lepidoptera: Bombycidae) suggest an origin in Southern Gondwana

Silkmoths (Bombycidae) have a disjunct distribution predominantly in the Southern Hemisphere and Asia. Here we reconstruct the phylogenetic history of the family to test competing hypotheses on their origin and assess how vicariance and long-distance dispersal shaped their current distribution. We sequenced up to 5,074 base pairs from six loci (COI, EF1-α, wgl, CAD, GAPDH, and RpS5) to infer the historical biogeography of Bombycidae. The multilocus dataset covering 20 genera (80 %) of the family, including 17 genera (94 %) of Bombycinae and 3 genera (43 %) of Epiinae, was used to estimate phylogenetic patterns, divergence times and biogeographic reconstruction. Dating estimates extrapolated from secondary calibration sources indicate the Bombycidae stem-group originated approximately 64 Mya. The subfamilies Epiinae (South America) and Bombycinae (Australia, Asia, East Palaearctic, and Africa) were reciprocally monophyletic, diverging at c. 56 Mya (95 % credibility interval: 66–46 Mya). The ‘basal’ lineage of Bombycinae — Gastridiota + Elachyophtalma — split from the rest of Bombycinae c. 53 Mya (95 % credibility interval: 63–43 Mya). Gastridiota is a monobasic genus with a relictual distribution in subtropical forests of eastern Australia. The Oriental and African genera comprised a monophyletic group: the Oriental region was inferred to have been colonized from a long-distance dispersal event from Australia to South-East Asia c. 53 Mya or possibly later (c. 36–26 Mya); Africa was subsequently colonized by dispersal from Asia c. 16 Mya (95 % credibility interval: 21–12 Mya). Based on the strongly supported phylogenetic relationships and estimates of divergence times, we conclude that Bombycidae had its origin in the fragment of Southern Gondwana consisting of Australia, Antarctica and South America during the Paleocene. The disjunction between South America (Epiinae) and Australia (Bombycinae) is best explained by vicariance in the Eocene, whereas the disjunct distribution in Asia and Africa is best explained by more recent dispersal events.

Transcriptome sequencing data provides a solid base to understand the phylogenetic relationships, biogeography and reticulated evolution of the genus Zamia L. (Cycadales: Zamiaceae).

Cycad is a key lineage to understand the early evolution of seed plants and their response to past environmental changes. However, tracing the evolutionary trajectory of cycad species is challenging when the robust relationships at inter- or infrageneric level are not well resolved. Here, using 2,901 single-copy nuclear genes, we explored the species relationships and gene flow within the second largest genus of cycads, i.e., Zamia, based on phylotranscriptomic analyses of 90% extant Zamia species. Based on a well-resolved phylogenetic framework, we performed gene flow analyses, molecular dating, and biogeographical reconstruction to examine the spatiotemporal evolution of Zamia. We also performed ancestral state reconstruction (ASR) of a total of 62 traits of the genus to comprehensively investigate its morphological evolution. Zamia is comprised of seven major clades corresponding to seven distinct distribution areas in the Americas, with at least three reticulation nodes revealed in this genus. Extant lineages of Zamia initially diversified around 18.4-32.6 (29.14) million years ago (MA) in the Mega-Mexico, and then expanded eastward into the Caribbean and southward into Central and South America. ASR revealed homoplasy in most of the morphological characters. This study revealed congruent phylogenetic relationships from comparative methods/datasets, with some conflicts being the result of incomplete lineage sorting and ancient/recent hybridization events. The strong association between the clades and the biogeographic areas suggested that ancient dispersal events shaped the modern distribution pattern, and regional climatic factors may have resulted in the following in-situ diversification. Climate cooling starting during the mid Miocene is associated with the global expansion of Zamia to the tropical South America that have dramatically driven lineage diversification in the New World flora, as well as the extinction of cycad species in the nowadays cooler regions of both hemispheres as indicated by the fossil records.

Phylogenomics and biogeography of the small carpenter bees (Apidae: Xylocopinae: Ceratina)

Small carpenter bees in the genus Ceratina are behaviourally diverse, species-rich, and cosmopolitan, with over 370 species and a range including all continents except Antarctica. Here, we present the first comprehensive phylogeny of the genus based on ultraconserved element (UCE) phylogenomic data, covering a total of 185 ingroup specimens representing 22 of the 25 current subgenera. Our results support most recognized subgenera as natural groups, but we also highlight several groups in need of taxonomic revision – particularly the nominate subgenus Ceratina sensu stricto – and several clades that likely need to be described as new subgenera. In addition to phylogeny, we explore the evolutionary history of Ceratina through divergence time estimation and biogeographic reconstruction. Our findings suggest that Ceratinini split from its sister tribe Allodapini about 72 million years ago. The common ancestor of Ceratina emerged in the Afrotropical realm approximately 42 million years ago, near the Middle Eocene Climatic Optimum. Multiple subsequent dispersal events led to the present cosmopolitan distribution of Ceratina, with the majority of transitions occurring between the Afrotropics, Indomalaya, and the Palearctic. Additional movements also led to the arrival of Ceratina in Madagascar, Australasia, and a single colonization of the Americas. Dispersal events were asymmetrical overall, with temperate regions primarily acting as destinations for migrations from tropical source regions.

Discovery of an endemism hotspot of freshwater mussels (Bivalvia: Unionidae) in Assam, with a description of two new genera

Abstract The Indian subcontinent houses a unique fauna of freshwater mussels. Tectonic and biogeographic reconstructions indicate that this fauna represents a derivative of Mesozoic Gondwanan biota and that it arrived in Asia on the Indian Plate, using this tectonic block as a ‘biotic ferry’. Though a preliminary integrative revision of the Indian Unionidae was published recently, the level of endemism and taxonomic richness of regional assemblages are unsatisfactorily known. Here, we revise the taxonomy of freshwater mussels from the Brahmaputra River basin based on a large DNA-sequence and morphological dataset that was sampled in Assam, north-eastern India. We managed to collect and sequence topotypes for nearly all nominal species described from the region, except for Lamellidens friersoni and Parreysia smaragdites. Our phylogenetic and morphology-based research reveals that the regional Unionidae assemblage contains nine species, belonging to a single subfamily, the Parreysiinae. Seven species and three genera (Balwantia, Pseudoscabies Bolotov, Sonowal, Kardong, Pasupuleti and Subba Rao gen. nov., and Assamnaia Bolotov, Sonowal, Kardong, Pasupuleti and Subba Rao gen. nov.) appear to be endemic to the region, indicating that the Brahmaputra River may represent an endemism hotspot of global significance. Our findings highlight that this region should be considered a high-priority area for freshwater conservation management.

A revised phylogeny of Boletaceae using whole genome sequences

ABSTRACT The porcini mushroom family Boletaceae is a diverse, widespread group of ectomycorrhizal (ECM) mushroom-forming fungi that so far has eluded intrafamilial phylogenetic resolution based on morphology and multilocus data sets. In this study, we present a genome-wide molecular data set of 1764 single-copy gene families from a global sampling of 418 Boletaceae specimens. The resulting phylogenetic analysis has strong statistical support for most branches of the tree, including the first statistically robust backbone. The enigmatic Phylloboletellus chloephorus from non-ECM Argentinian subtropical forests was recovered as a new subfamily sister to the core Boletaceae. Time-calibrated branch lengths estimate that the family first arose in the early to mid-Cretaceous and underwent a rapid radiation in the Eocene, possibly when the ECM nutritional mode arose with the emergence and diversification of ECM angiosperms. Biogeographic reconstructions reveal a complex history of vicariance and episodic long-distance dispersal correlated with historical geologic events, including Gondwanan origins and inferred vicariance associated with its disarticulation. Together, this study represents the most comprehensively sampled, data-rich molecular phylogeny of the Boletaceae to date, establishing a foundation for future robust inferences of biogeography in the group.

Phylogenetics, character evolution, and historical biogeography of the Neotropical genus Besleria (Gesneriaceae)

Abstract Besleria, a genus of perennial herbs, shrubs, or small trees growing in the understorey of rainforests, is one of the largest genera of neotropical Gesneriaceae, with over 165 species. Despite the ecological importance and ubiquity of Besleria in rainforest ecosystems, taxonomic and evolutionary studies of Besleria are limited. Here, we generated a phylogenetic analysis of Besleria using four nuclear and chloroplast DNA regions (ITS, matK, rps16, and trnL-trnF) covering more than 50% of the recognized species, along with two secondary calibration points to infer divergence times. Our results support the monophyly of Besleria and allowed us to revise the infrageneric classification and biogeographical history of the genus. We identified five major clades that do not correspond to sections or subsections in previous classifications. These clades are well circumscribed geographically but remain difficult to characterize using previously hypothesized morphological characters. Biogeographical reconstructions indicate an origin in the northern Andes during the Middle Miocene (ca. 15 Mya). The current distribution patterns of this plant group have been significantly shaped by geological and climatic events, particularly Andean uplift and the formation of the Panama Isthmus.

Bayesian tip-dated phylogeny and biogeography of Cissampelideae (Menispermaceae): Mitigating the effects of homoplastic morphological characters.

The integration of morphological and molecular data is essential to understand the affinities of fossil taxa and spatio-temporal evolutionary processes of organisms. However, homoplastic morphological characters can mislead the placement of fossil taxa and impact downstream analyses. Here, we provide an example of how to mitigate effectively the effect of morphological homoplasy on the placement of fossil taxa and biogeographic inferences of Cissampelideae. We assembled three data types, morphological data only, morphological data with a molecular scaffold and combined morphological and molecular data. By removing high-level homoplastic morphological data or reweighting the morphological characters, we conducted 15 parsimony, 12 undated Bayesian and four dated Bayesian analyses. Our results show that the 14 selected Cissampelideae fossil taxa are placed poorly when based only on morphological data, but the addition of molecular scaffold and combination of morphological and molecular data greatly improve the resolution of fossil nodes. We raise the monotypic Stephania subg. Botryodiscia to generic status and discover that three fossils previously assigned to Stephania should be members of Diploclisia. The Bayesian tip-dated tree recovered by removing homoplastic morphological characters with a Rescaled Consistency Index <0.25 has the highest stratigraphic fit and consequently generates more reasonable biogeographic reconstruction for Cissampelideae. Cissampelideae began to diversify in Asia in the latest Cretaceous and subsequently dispersed to South America around the Cretaceous-Palaeogene boundary. Two dispersal events from Asia to Africa occurred in the Early Eocene and the Late Eocene-Late Oligocene, respectively. These findings provide guidelines and practical methods for mitigating the effects of homoplastic morphological characters on fossil placements and Bayesian tip-dating, as well as insights into the past tropical floristic exchanges among different continents.

Biogeographic history of Pterocarya (Juglandaceae) inferred from phylogenomic and fossil data

AbstractPterocarya (Juglandaceae) is disjunctly distributed in East Asia and the Caucasus region today, but its fossils are widely distributed in the Northern Hemisphere. We first inferred phylogeny with time estimation of Pterocarya under node‐dating (ND) based on plastomes of all eight extant species and tip‐dating (TD) based on plastomes and 69 morphological characters of 19 extant and extinct species, respectively. We compared the biogeographical reconstructions on the timetrees from ND and TD, respectively, and then compiled 83 fossil records and 599 current occurrences for predicting the potential distributions for the past and the future. The most recent comment ancestor of Pterocarya is inferred in East Asia at 40.46 Ma (95% highest posterior density [HPD]: 28.04–54.86) under TD and 26.81 Ma (95% HPD: 23.03–33.12) under ND. The current distribution was attributed to one dispersal and one vicariant event without fossils, but as many as six dispersal, six vicariant, and 11 local extinction events when considering fossils. Pterocarya migrated between East Asia and North America via the Bering Land Bridge during the early Oligocene and the early Miocene periods. With the closure of Turgai Strait, Pterocarya dispersed between East Asia and Europe through the Miocene. The potential distribution analyses indicated that Pterocarya preferred warm temperate regions across the Northern Hemisphere since the Oligocene, but the drastic temperature decline caused its extinction in high latitudes. Except for Pterocarya fraxinifolia and Pterocarya stenoptera, suitable habitats for this genus are predicted to contract by 2070 due to climate change.

Comparative plastome assembly of the yellow ironweed (Verbesina alternifolia) using Nanopore and Illumina reads.

Chloroplast genomes (plastomes) represent a very important source of valuable information for phylogenetic and biogeographic reconstructions. The use of short reads (as those produced from Illumina sequencing), along with de novo read assembly, has been considered the "gold standard" for plastome reconstruction. However, short reads often cannot reconstruct long repetitive regions in chloroplast genomes. Long Nanopore (ONT) reads can help bridging long repetitive regions but are by far more error-prone than those produced by Illumina sequencing. Verbesina is the largest genus of tribe Heliantheae (Asteraceae) and includes species of economic importance as ornamental or as invasive weeds. However, no complete chloroplast genomes have been published yet for the genus. We utilized Illumina and Nanopore sequencing data and different assembly strategies to reconstruct the plastome of Verbesina alternifolia and evaluated the usefulness of the Nanopore assemblies. The two plastome sequence assemblages, one obtained with the Nanopore sequencing and the other inferred with Illumina reads, were identical, except for missing bases in homonucleotide regions. The best-assembled plastome of V. alternifolia was 152,050 bp in length and contained 80, 29, and four unique protein-coding genes, tRNAs, and rRNAs, respectively. When used as reference for mapping Illumina reads, all plastomes performed similarly. In a phylogenetic analysis including 28 other plastomes from closely related taxa (from the Heliantheae alliance), the two Verbesina chloroplast genomes grouped together and were nested among the other members of the tribe Heliantheae s.str. Our study highlights the usefulness of the Nanopore technology for assembling rapidly and cost-effectively chloroplast genomes, especially in taxonomic groups with paucity of publicly available plastomes.

Mitogenomic phylogeny, biogeography, and cryptic divergence of the genus Silurus (Siluriformes: Siluridae).

The genus Silurus, an important group of catfish, exhibits heterogeneous distribution in Eurasian freshwater systems. This group includes economically important and endangered species, thereby attracting considerable scientific interest. Despite this interest, the lack of a comprehensive phylogenetic framework impedes our understanding of the mechanisms underlying the extensive diversity found within this genus. Herein, we analyzed 89 newly sequenced and 20 previously published mitochondrial genomes (mitogenomes) from 13 morphological species to reconstruct the phylogenetic relationships, biogeographic history, and species diversity of Silurus. Our phylogenetic reconstructions identified eight clades, supported by both maximum-likelihood and Bayesian inference. Sequence-based species delimitation analyses yielded multiple molecular operational taxonomic units (MOTUs) in several taxa, including the Silurus asotus complex (four MOTUs) and Silurus microdorsalis (two MOTUs), suggesting that species diversity is underestimated in the genus. A reconstructed time-calibrated tree of Silurus species provided an age estimate of the most recent common ancestor of approximately 37.61 million years ago (Ma), with divergences among clades within the genus occurring between 11.56 Ma and 29.44 Ma, and divergences among MOTUs within species occurring between 3.71 Ma and 11.56 Ma. Biogeographic reconstructions suggested that the ancestral area for the genus likely encompassed China and the Korean Peninsula, with multiple inferred dispersal events to Europe and Central and Western Asia between 21.78 Ma and 26.67 Ma and to Japan between 2.51 Ma and 18.42 Ma. Key factors such as the Eocene-Oligocene extinction event, onset and intensification of the monsoon system, and glacial cycles associated with sea-level fluctuations have likely played significant roles in shaping the evolutionary history of the genus Silurus.

Comparative phylogeography of two codistributed species of the genus Herichthys (Actinopterygii: Cichliformes: Cichlidae) in northeastern Mexico

Phylogeographic patterns of freshwater fishes in coastal regions are highly susceptible to eustatic sea level changes associated with Pleistocene glaciations. In this context, the Plain Coastal Gulf in northeastern Mexico represents an ideal study area due to its low elevation. Herein, we compare the phylogeographic structures of two cichlid species of the genus Herichthys Baird et Girard, 1854 widely distributed in the Pánuco–Tamesí system in northeastern Mexico using two mitochondrial markers. The species studied were: Herichthys carpintis (Jordan et Snyder, 1899) and Herichthys pantostictus (Taylor et Miller, 1983). We estimate their genetic diversity, gene flow, and demographic history and perform biogeographic reconstructions using a Bayesian computation approach and environmental niche modeling. The biogeographic reconstruction suggests a different history for each species. Environmental niche modeling indicates that both species experienced a demographic expansion during the Pleistocene but responded differently to Pleistocene climatic changes. In summary, their current sympatric distribution could be the outcome of contemporary and not historical processes reflecting a pseudo-incongruent pattern.

Bayesian Total-Evidence Dating Revisits Sloth Phylogeny and Biogeography: A Cautionary Tale on Morphological Clock Analyses.

Combining morphological and molecular characters through Bayesian total-evidence dating allows inferring the phylogenetic and timescale framework of both extant and fossil taxa, while accounting for the stochasticity and incompleteness of the fossil record. Such an integrative approach is particularly needed when dealing with clades such as sloths (Mammalia: Folivora), for which developmental and biomechanical studies have shown high levels of morphological convergence whereas molecular data can only account for a limited percentage of their total species richness. Here, we propose an alternative hypothesis of sloth evolution that emphasizes the pervasiveness of morphological convergence and the importance of considering the fossil record and an adequate taxon sampling in both phylogenetic and biogeographic inferences. Regardless of different clock models and morphological datasets, the extant sloth Bradypus is consistently recovered as a megatherioid, and Choloepus as a mylodontoid, in agreement with molecular-only analyses. The recently extinct Caribbean sloths (Megalocnoidea) are found to be a monophyletic sister-clade of Megatherioidea, in contrast to previous phylogenetic hypotheses. Our results contradict previous morphological analyses and further support the polyphyly of "Megalonychidae," whose members were found in five different clades. Regardless of taxon sampling and clock models, the Caribbean colonization of sloths is compatible with the exhumation of islands along Aves Ridge and its geological time frame. Overall, our total-evidence analysis illustrates the difficulty of positioning highly incomplete fossils, although a robust phylogenetic framework was recovered by an a posteriori removal of taxa with high percentages of missing characters. Elimination of these taxa improved topological resolution by reducing polytomies and increasing node support. However, it introduced a systematic and geographic bias because most of these incomplete specimens are from northern South America. This is evident in biogeographic reconstructions, which suggest Patagonia as the area of origin of many clades when taxa are underrepresented, but Amazonia and/or Central and Southern Andes when all taxa are included. More generally, our analyses demonstrate the instability of topology and divergence time estimates when using different morphological datasets and clock models and thus caution against making macroevolutionary inferences when node support is weak or when uncertainties in the fossil record are not considered.

Evolutionary history of Castanea sativa in the Caucasus driven by Middle and Late Pleistocene paleoenvironmental changes.

Due to global climate cooling and aridification since the Paleogene, members of the Neogene flora were extirpated from the Northern Hemisphere or were confined to a few refugial areas. For some species, the final reduction/extinction came in the Pleistocene, but some others have survived climatic transformations up to the present. This has occurred in Castanea sativa, a species of high commercial value in Europe and a significant component of the Caucasian forests' biodiversity. In contrast to the European range, neither the historical biogeography nor the population genetic structure of the species in its isolated Caucasian range has been clarified. Here, based on a survey of 21 natural populations from the Caucasus and a single one from Europe, we provide a likely biogeographic reconstruction and genetic diversity details. By applying Bayesian inference, species distribution modelling and fossil pollen data, we estimated (i) the time of the Caucasian-European divergence during the Middle Pleistocene, (ii) the time of divergence among Caucasian lineages and (iii) outlined the glacial refugia for species. The climate changes related to the Early-Middle Pleistocene Transition are proposed as the major drivers of the intraspecific divergence and European-Caucasian disjunction for the species, while the impact of the last glacial cycle was of marginal importance.

Macroevolutionary consequences of karyotypic changes in the neotropical Serrasalmidae fishes (Ostariophysi, Characiformes) diversification.

In the Neotropical region, one of the most diverse families of freshwater fishes is the monophyletic Serrasalmidae. Karyotypically, the family shows high diversity in chromosome numbers (2n = 54 to 64). However, little is discussed about whether the chromosomal changes are associated with cladogenetic events within this family. In the present study, we evaluated the role of chromosomal changes in the evolutionary diversification of Serrasalmidae. Our phylogenetic sampling included 36 species and revealed three main clades. The ancestral chromosome number reconstruction revealed the basic number 2n = 54 and a high frequency of ascending dysploid events in the most derived lineages. Our biogeographic reconstruction suggests an Amazonian origin of the family at 48-38 Mya, with independent colonization of other basins between 15 and 8 Mya. We did not find specific chromosomal changes or increased diversification rates correlated with the colonization of a new environment. On the other hand, an increase in the diversification rate was detected involving the genus Serrasalmus and Pygocentrus in the Miocene, correlated with the stasis of 2n = 60. Our data demonstrate that chromosomal rearrangements might have played an important evolutionary role in major cladogenetic events in Serrasalmidae, revealing them as a possible evolutionary driver in their diversification.

Reconstructing ancient dispersal through Antarctica: A case study of stream‐inhabiting beetles

AbstractAimAlthough Antarctica hosted a diverse fauna and flora in the past, its modern climate is too extreme for many lineages: their recent extinction makes it difficult to include the continent in historical biogeographical analyses. We use southern temperate stream‐inhabiting beetles as a model to explore whether Antarctica may be included in historical biogeographic reconstructions in a group absent from Antarctica today, and to test its role in shaping the current distribution of stream‐inhabiting insects.TaxonColeoptera, Elmidae.LocationSouthern Hemisphere temperate regions and Antarctica.MethodsWe included Antarctica in historical biogeographic analyses indirectly, as a component of distance matrices specifying the relative positions of continents, or by specifying Antarctica as a stepping‐stone between remaining continents (in LEMAD). We used a newly constructed dated phylogeny of Elmidae to test the performance of these constrained analyses under different parameter settings and geographical scenarios.ResultsAntarctica can be implemented into historical biogeographic analyses via indirect constraints to produce biologically relevant reconstructions when long‐distance dispersal events are highly penalized, the maximum number of areas per species is low, and expected extinction rates are high (in LEMAD). Unconstrained models, including those without Antarctica, result in simpler scenarios with fewer biogeographic events and better fit to data. The origin of austral clades of Elmidae post‐date the separation of Gondwanan landmasses.Main ConclusionsAntarctica can be included in historical biogeographic reconstructions under a priori assumptions that (1) it was part of the ancient biogeography of the clade, (2) the taxon has limited dispersal ability, making long‐distance dispersal highly unlikely and (3) maximum range size is limited. These assumptions may be biologically justified for many animal groups. Over‐water dispersal has been crucial in shaping the modern distribution of austral stream‐inhabiting beetles, likely facilitated by ocean currents and dispersal through Antarctica until the Oligocene.

Crossing the Rift valley: using complete mitogenomes to infer the diversification and biogeographic history of ethiopian highlands Ptychadena (anura: Ptychadenidae).

The Ethiopian Highlands are considered a biodiversity hotspot, harboring a high number of endemic species. Some of the endemic species probably diversified in situ; this is, for example, the case of a monophyletic clade containing 12 known species of grass frogs of the genus Ptychadena. The different species occur at elevations ranging from 1,500 to above 3,400m and constitute excellent models to study the process of diversification in the highlands as well as adaptations to high elevations. In this study, we sampled 294 specimens across the distribution of this clade and used complete mitogenomes and genome-wide SNP data to better understand how landscape features influenced the population structure and dispersal of these grass frogs across time and space. Using phylogenetic inference, population structure analyses, and biogeographic reconstructions, we found that the species complex probably first diversified on the south-east side of the Great Rift Valley. Later on, species dispersed to the north-west side, where more recent diversification occurred. We further demonstrate that Ptychadena species have dispersed across the Great Rift Valley at different times. Our analyses allowed for a more complete understanding of the contribution of geological events, biogeographic barriers and climatic changes as drivers of species diversification and adaptation in this important biogeographic region.