Ancestral Area Reconstruction Research Articles

Of sea, rivers and symbiosis: Diversity, systematics, biogeography and evolution of the deeply diverging florideophycean order Hildenbrandiales (Rhodophyta)

The Hildenbrandiales, a typically saxicolous red algal order, is an early diverging florideophycean group with global significance in marine and freshwater ecosystems across diverse temperature zones. To comprehensively elucidate the diversity, phylogeny, biogeography, and evolution of this order, we conducted a thorough re-examination employing molecular data derived from nearly 700 specimens. Employing a species delimitation method, we identified Evolutionary Species Units (ESUs) within the Hildenbrandiales aiming to enhance our understanding of species diversity and generate the first time-calibrated tree and ancestral area reconstruction for this order. Mitochondrial cox1 and chloroplast rbcL markers were used to infer species boundaries, and subsequent phylogenetic reconstructions involved concatenated sequences of cox1, rbcL, and 18S rDNA. Time calibration of the resulting phylogenetic tree used a fossil record from a Triassic purportedly freshwater Hildenbrandia species and three secondary time points from the literature. Our species delimitation analysis revealed an astounding 97 distinct ESUs, quintupling the known diversity within this order. Our time-calibration analysis placed the origin of Hildenbrandiales (crown age) in the Ediacaran period, with freshwater species emerging as a monophyletic group during the later Permian to early Triassic. Phylogenetic reconstructions identified seven major clades, experiencing early diversification during the Silurian to Carboniferous period. Two major evolutionary events—colonization of freshwater habitats and obligate systemic symbiosis with a marine fungus—marked this order, leading to significant morphological alterations without a commensurate increase in species diversification. Despite the remarkable newly discovered diversity, the extant taxon diversity appears relatively constrained when viewed against an evolutionary timeline spanning over 800 million years. This limitation may stem from restricted geographic sampling or the prevalence of asexual reproduction. However, species richness estimation and rarefaction analyses suggest a substantially larger diversity yet to be uncovered—potentially four times greater. These findings drastically reshape our understanding of the deeply diverging florideophycean order Hildenbrandiales species diversity, and contribute valuable insights into this order evolutionary history and ecological adaptations. Supported by phylogenetic, ecological and morphological evidence, we established the genus Riverina gen. nov. to accommodate freshwater species of Hildenbrandiales, which form a monophyletic clade in our analyses. This marks the first step toward refining the taxonomy of the Hildenbrandiales order, a task demanding thorough revisions, notably the creation of several genera to address the polyphyletic status of Hildenbrandia. However, the limited diagnostic features pose a challenge, necessitating a fresh approach to defining genera. A potential solution lies in embracing a molecular systematic perspective, which can offer precise delineations of taxonomic boundaries.

Conserved DNA sequence analysis reveals the phylogeography and evolutionary events of Akebia trifoliata in the region across the eastern edge of the Tibetan Plateau and subtropical China

BackgroundThe eastern edge of the Qinghai‒Tibet Plateau (QTP) and subtropical China have various regions where plant species originate and thrive, but these regions have been the focus of very few integrative studies. Here, we elucidated the phylogeographic structure of a continuous and widespread Akebia trifoliata population across these two regions.ResultsSixty-one populations consisting of 391 genotypes were examined to assess population diversity and structure via network distribution analysis, maximum likelihood phylogenetic tree reconstruction, divergence time estimation, demographic history inference, and ancestral area reconstruction of both conserved internal transcribed spacer (ITS) and chloroplast (rps16) DNA sequences. The results showed that the ITS region was more variable than the rps16 region and could be suitable for studying intraspecific phylogeography. The A. trifoliata population displayed high genetic diversity, genetic differentiation and obvious phylogeographical structure, possibly originating on the eastern QTP, expanding during the last glacial-interglacial cycle, diverging in the early Pleistocene and middle Pleistocene, and extensively migrating thereafter. The migration route from west to east along rivers could be largely responsible for the long-distance dispersal of this species, while three main refuges (Qinba Mountains, Nanling Mountains and Yunnan-Guizhou Plateau) with multiple ice shelters facilitated its wide distribution.ConclusionsOur results suggested that the from west to east long migration accompanying with the minor short reciprocal migration in the south-north direction, and the three main refuges (the Qinba Mountains, Nanling Mountains and Yunnan-Guizhou Plateau) contributed to the extant geographical distribution of A. trifoliata. In addition, this finding also strongly reduced the discrepancy between glacial contraction and postglacial expansion and the in situ survival hypothesis by simultaneously considering the existence of many similar climate-related ecological niches and migration influences.

Genetic differentiation and phylogeography of Erythroneurini (Hemiptera, Cicadellidae, Typhlocybinae) in the southwestern karst area of China.

Erythroneurini is the largest tribe of the microleafhopper subfamily Typhlocybinae. Most prior research on this tribe has focused on traditional classification, phylogeny, and control of agricultural pests, and the phylogeography of the group remains poorly understood. In this study, the mitochondrial genomes of 10 erythroneurine species were sequenced, and sequences of four genes were obtained for 12 geographical populations of Seriana bacilla. The new sequence data were combined with previously available mitochondrial DNA sequence data and analyzed using Bayesian and Maximum-Likelihood-based phylogenetic methods to elucidate relationships among genera and species and estimate divergence times. Seriana was shown to be derived from within Empoascanara. Phylogeographic and population genetic analysis of the endemic Chinese species Seriana bacilla suggest that the species diverged about 54.85 Mya (95% HPD: 20.76-66.23 million years) in the Paleogene period and that population divergence occurred within the last 14 million years. Ancestral area reconstruction indicates that Seriana bacilla may have originated in the central region of Guizhou, and geographical barriers are the main factors affecting gene flow among populations. Ecological niche modeling using the MaxEnt model suggests that the distribution of the species was more restricted in the past but is likely to expand in the future years 2050 and 2070.

Let's get high: Cladogenesis in freshwater crabs (Decapoda: Potamonautidae: Potamonautes) supports the mountain gradient speciation hypothesis in the Cape Fold and Drakensberg Mountains, South Africa.

During the present study, the evolutionary relationship within a clade of mountain clade of freshwater crabs (Potamonautes) was examined using mtDNA sequence data for species from the Cape Fold Mountain (CFM) and Great Escarpment (Drakensberg Mountain range). We undertook phylogenetic analyses, divergence time estimation, and an ancestral area reconstruction to explore the period of cladogenesis and understand the biogeographic history in this high-altitude clade. Furthermore, we applied four species delimitation methods using ASAP, bPTP, bGMYC, and STACEY on the latter clade. Bayesian phylogenetic analyses retrieved a monophyletic freshwater crab clade comprised of two major sister clades, one comprised of the Cape Fold (clade A) and two comprised of Drakensberg Mountains (clade B) species. Divergence time estimation indicated that the two clades underwent Mio/Pliocene cladogenesis. Within the CFM clade (A), P. amathole (Amathola Mountains) was sister to P. parvispina (Cederberg and Kouebokkeveld Mountains) and the latter species were sister to P. parvicorpus (Cape Peninsula, Jonkershoek, and Helderberg Mountains) sister to P. tuerkayi (Overberg Mountains) and P. brincki (Hottentots Holland Mountains). Within the Drakensberg Mountain clade (B), we observed in situ diversification. Specimens from the southcentral Drakensberg Mountains (Dargle Forest, Injasuti, Karkloof, and Impendle) represent a new undescribed lineage Potamonautes sp. nov. 1. The second clade from the northern Drakensberg, representing P. clarus, was sister to a central Drakensberg Mountain clade that comprised P. depressus that was in turn sister to P. baziya from the Eastern Cape Province. The application of species delimitation methods generally overestimated the number of species. The biogeographic analyses indicated that the Eastern Cape Province is the most likely ancestral range area. Ecological niche modelling of representative species in clades A (Cape Fold Mountains) and B (Drakensberg Mountains) demonstrated that temperature and rainfall were the major abiotic drivers that differentiated the two clades. Our data favours the mountain gradient speciation hypothesis.

Some like it hot: Past and present phylogeography of a desert dwelling gecko across the Arabian Peninsula

AbstractAimDeserts represent dynamic ecosystems that support communities of endemic and specialised species. We analysed the role of present and past climatic conditions in shaping the distribution of the widespread Bunopus geckos in the Arabian and south‐west Asian deserts. We studied their phylogeographic and demographic history to test whether the Bunopus geckos colonised Arabia from Asia or, vice versa, Asia from Arabia and to identify migration corridors that have historically enabled the dispersal of Bunopus geckos.LocationThe Middle East, especially the Arabian Peninsula.TaxonGenus Bunopus (Squamata; Gekkonidae).MethodsWe generated sequence data for four genes and performed maximum likelihood, Bayesian inference and time‐calibrated phylogenetic analyses and ancestral area reconstruction to infer the phylogenetic and biogeographic history of the genus. We modelled the species' distribution and projected it to several past time periods spanning from mid‐Pliocene to the present. We analysed contemporary landscape connectivity across the peninsula to identify dispersal corridors that enable migration and promote gene flow among Bunopus populations in Arabia.ResultsBunopus is formed by deeply divergent lineages that correspond to up to eight candidate species. The genus originated in southwest Asia and dispersed to Arabia in the late Miocene. The Arabian populations were stable through most of their history in terms of size and distribution extent. Major corridors for contemporary Bunopus dispersal stretch along the eastern Arabian coasts from where they cross through the peninsula to the northern Red Sea coasts.Main ConclusionsThe evolutionary history of Bunopus was substantially influenced by paleoenvironmental conditions. The generalist habits and ground‐dwelling lifestyle enabled the geckos to colonise most of the arid regions of southwest Asia, with Arabia being colonised from the Iranian Plateau in the late Miocene. The distribution extent of Bunopus responded to the past climatic and habitat oscillations; the range was fragmented during moist climatic phases, and it expanded in times of increased aridity. The genus requires taxonomic revision to formally assess its diversity. Based on the results obtained in this study, Crossobamon orientalis is reassigned to Bunopus.

From forest to savanna and back to forest: Evolutionary history of the genus Dimorphandra (Fabaceae).

The tree genus Dimorphandra (Fabaceae), which contains 26 species divided into three subgenera, was studied using DNA sequence data from six chloroplast genome regions (cpDNA) and the nuclear internal transcribed spacer (ITS). The analyses, which included Bayesian phylogenies and haplotype networks, ancestral area reconstructions, and ecological niche modeling, allowed for exploring the evolutionary history of Dimorphandra. Within the subgenus Phaneropsia, the cpDNA sequence data were more closely-related to species from the genus Mora, while the ITS sequence data displayed a closer phylogenetic relationship with the subgenus Pocillum. This incongruence may be due to incomplete lineage sorting associated with ancient polymorphisms. The Amazonian Dimophandra lineages were highly polymorphic and divergent, while those from the Cerrado and the Atlantic Forest had low levels of polymorphisms. The Amazon likely gave rise to the Dimophandra lineage that produced the Cerrado species, while a Cerrado lineage likely gave rise to the Atlantic Forest species. Habitat shifts were identified as a key factor in shaping the late evolutionary history of Dimorphandra.

The use of an integrated framework combining eco-evolutionary data and species distribution models to predict range shifts of species under changing climates

Species distribution models (SDMs) are powerful tools that can predict potential distributions of species under climate change. However, traditional SDMs that rely on current species occurrences may underestimate their climatic tolerances and potential distributions. To address this limitation, we developed an integrated framework that incorporates eco-evolutionary data into SDMs. In our approach, the fundamental niches of species are constructed by their realized niches in different periods, and those fundamental niches are used to predict potential distributions of species. Our framework includes multiple phylogenetic analyses, such as niche evolution rate estimation and ancestral area reconstruction. These analyses provide deeper insights into the responses of species to climate change. We applied our approach to the Chrysanthemum zawadskii species complex to evaluate its efficacy through comprehensive performance evaluations and validation tests. Our framework can be applied broadly to species with available phylogenetic data and occurrence records, making it a valuable tool for understanding species adaptation in a rapidly changing world.•Integrating the niches of species in different periods estimates more complete climatic envelopes for them.•Combining eco-evolutionary data with SDMs predicts more comprehensive potential distributions of species under climate change.•Our framework provides a general procedure for species with phylogenetic data and occurrence records.

Biogeography of Greater Antillean freshwater fishes, with a review of competing hypotheses.

In biogeography, vicariance and long-distance dispersal are often characterised as competing scenarios. However, they are related concepts, both relying on collective geological, ecological, and phylogenetic evidence. This is illustrated by freshwater fishes, which may immigrate to islands either when freshwater connections are temporarily present and later severed (vicariance), or by unusual means when ocean gaps are crossed (long-distance dispersal). Marine barriers have a strong filtering effect on freshwater fishes, limiting immigrants to those most capable of oceanic dispersal. The roles of vicariance and dispersal are debated for freshwater fishes of the Greater Antilles. We review three active hypotheses [Cretaceous vicariance, Greater Antilles-Aves Ridge (GAARlandia), long-distance dispersal] and propose long-distance dispersal to be an appropriate model due to limited support for freshwater fish use of landspans. Greater Antillean freshwater fishes have six potential source bioregions (defined from faunal similarity): Northern Gulf of México, Western Gulf of México, Maya Terrane, Chortís Block, Eastern Panamá, and Northern South America. Faunas of the Greater Antilles are composed of taxa immigrating from many of these bioregions, but there is strong compositional disharmony between island and mainland fish faunas (>90% of Antillean species are cyprinodontiforms, compared to <10% in Northern Gulf of México and Northern South America, and ≤50% elsewhere), consistent with a hypothesis of long-distance dispersal. Ancestral-area reconstruction analysis indicates there were 16 or 17 immigration events over the last 51 million years, 14 or 15 of these by cyprinodontiforms. Published divergence estimates and evidence available for each immigration event suggests they occurred at different times and by different pathways, possibly with rafts of vegetation discharged from rivers or washed to sea during storms. If so, ocean currents likely provide critical pathways for immigration when flowing from one landmass to another. On the other hand, currents create dispersal barriers when flowing perpendicularly between landmasses. In addition to high salinity tolerance, cyprinodontiforms collectively display a variety of adaptations that could enhance their ability to live with rafts (small body size, viviparity, low metabolism, amphibiousness, diapause, self-fertilisation). These adaptations likely also helped immigrants establish island populations after arrival and to persist long term thereafter. Cichlids may have used a pseudo bridge (Nicaragua Rise) to reach the Greater Antilles. Gars (Lepisosteidae) may have crossed the Straits of Florida to Cuba, a relatively short crossing that is not a barrier to gene flow for several cyprinodontiform immigrants. Indeed, widespread distributions of Quaternary migrants (Cyprinodon, Gambusia, Kryptolebias), within the Greater Antilles and among neighbouring bioregions, imply that long-distance dispersal is not necessarily inhibitory for well-adapted species, even though it appears to be virtually impossible for all other freshwater fishes.

Mapping species richness and evolutionary regions of the genus Myrcia

AbstractAimMyrcia is a plant genus exclusive of the Neotropical region and one of the most important components of the tree diversity in the Cerrado and Atlantic Forest domains. However, no mapping of its taxonomic diversity for this region exists. Our aim was to describe the spatial patterns of diversity and biogeographical history for Myrcia in the Neotropical region based on a phylogenetic regionalization.LocationNeotropics.TaxonGenus Myrcia (Myrtaceae).MethodsWe derived distributions for 307 species from occurrence records using buffering and species distribution modelling. We used stacked distributions to generate a richness map of the genus and its clades (sections). In addition, we used phylogenetic regionalization methods to define evolutionary regions (evoregions) and ancestral area reconstruction to reveal the biogeographical history across these evoregions.ResultsWe found high species richness in the Atlantic Forest and Cerrado, with some sections restricted to the East coast of South America, while others were widespread across the Neotropics. We defined five evoregions, named A–E; the ancestral reconstruction revealed that Myrcia originated in evoregion B, under a tropical climate, with further specialization of distant‐related lineages to the colder environmental condition in evoregion A.Main ConclusionsHigh species richness of Myrcia in South America eastern coast and in the Brazilian highlands coincides with the evoregions with most diversification. Our genus‐specific regionalization together with the ancestral area reconstruction showed that evoregions A and B were the main evolutionary regions where diversification took place. In addition, the biogeographical history of the group suggests that some lineages have adaptations to deal with colder environments, that probably evolved in response to cooling periods since the mid‐Miocene.

Population Structure and Genetic Diversity Analyses Provide New Insight into the Endemic Species Aster spathulifolius Maxim. and Its Evolutionary History.

Aster spathulifolius, an ecologically significant plant species native to the coastal regions of Korea and Japan, remains understudied in terms of its genetic structure and evolutionary history. In this study, we employed four chloroplast markers and the nuclear ITS region from 15 populations of A. spathulifolius from both Korea and Japan, including their islands, to unravel the spatial genetic structure, differentiation, gene flow, phylogenetic, and biogeographical relationships. Analysis based on multiple methods identified a low level of genetic diversity, genetic differentiation and gene flow among A. spathulifolius populations. Network analysis and principal coordinates analysis showed that 15 populations could be divided into two groups: mainland and island. Furthermore, UPGMA, neighbor-net, maximum-likelihood and Bayesian inference-based phylogenetic tree confirmed that these populations formed two distinct clades. Therefore, the island populations might be treated as A. spathulifolius populations rather than A. oharai populations. Divergence time analysis estimated the divergence of A. spathulifolius lineages approximately 23.09 million years ago, while ancestral area reconstruction analysis suggested Korea as the potential origin, conflicting with alternative scenarios. These findings contribute to a comprehensive understanding of the evolutionary history, genetic structure, and adaptive strategies of A. spathulifolius in coastal environments. Our study challenges previous assumptions and underscores the necessity for further population studies to elucidate the intricate dynamics of this distinctive plant species.

Dispersal sweepstakes: Biotic interchange propelled air‐breathing fishes across the globe

AbstractAimBiotic interchanges between Africa, India, and Eurasia are central to explaining the present‐day distribution and diversity of freshwater organisms across these landmasses. Synbranchiformes is a diverse and species‐rich clade of freshwater acanthomorph fishes found on all southern continents except Antarctica, and include eel‐ and perch‐like, air‐breathing and non‐air‐breathing fishes. Lacking a comprehensive and resolved phylogeny of the entire clade, contemporary interpretations of synbranchiform biogeography invoke scenarios as disparate as Gondwanan vicariance and pan‐global rafting to explain their modern‐day distribution. Here, we study their biogeographic history of continental dispersal events and test whether these are associated with increases in lineage diversification.LocationAsia, India, Africa freshwater habitats.TaxonSynbranchiformes (gouramis, snakeheads, swamp eels, and relatives).MethodsWe used nearly 1000 ultra‐conserved elements (UCEs) and Sanger‐sequenced genes to infer a phylogeny with representatives of all major synbranchiform lineages and nearly two‐thirds of its known species diversity. Incorporating fossil calibrations, we inferred a time‐calibrated phylogeny to which we apply Bayesian methods of ancestral area reconstruction and test for diversification rate shifts.ResultsAnalyses of UCE data provide a resolved phylogeny for major synbranchiform lineages. Divergence times support a most recent common ancestor of the entire clade approximately 79.2 million years ago. We infer significant increases in lineage diversification in both the spiny eels (Mastacembelidae) and the genus Betta (Osphronemidae).Main ConclusionsOur results reject the hypothesis of Gondwanan vicariance explaining synbranchiform biogeography. Instead, our analyses reconstruct a southeast Asian origin of the entire clade and independent dispersal events to other continents by snakeheads, anabantids, and spiny eels, with no signal of elevated lineage diversification occurring after these invasions. Higher lineage diversification rates in spiny eels pre‐date their arrival to Africa, while the high diversification rates observed in Betta were initiated prior to the flooding of insular Sundaland in southeast Asia.

Biogeographic analysis based on phylogenomic data supports multiple ancient dispersals that facilitated the eastern Asia–North America–Mexico disjunction in the subfamily Linnaeoideae (Caprifoliaceae)

AbstractThe small subfamily Linnaeoideae of Caprifoliaceae exhibits a disjunct distribution in Eurasia and North America, including Mexico, with most taxa occurring in eastern Asia or Mexico and the monospecific Linnaea Gronov. ex L. having a circumboreal to north temperate distribution. We sampled 17 of the 20 species representing all Linnaeoideae genera and used nuclear (target enrichment) and complete plastome sequence data to reconstruct the phylogeny. Our results show strong topological conflicts between nuclear and plastid data, especially concerning Dipelta Maxim. and Diabelia Landrein, supporting hybridization events complicating the deep diversification. Nuclear data were used for divergence time estimation and ancestral area reconstruction. The divergence time between the Mexican Vesalea M. Martens &amp; Galeotti and the Linnaea clade was dated to 39.5 Ma, with a 95% highest posterior density of 28.2 Ma (mid‐Oligocene) to 45.2 Ma (mid‐Eocene). Reconstructed ancestral areas support a widespread common ancestor of Linnaea plus Vesalea in Mexico and at least another area (eastern Asia, North America, or Europe). The biogeographic analysis, including fossils, supports the ancestral range of Linnaeoideae to be widespread in central and western China + Europe + Mexico, or eastern and northern Asia + central and western China + Mexico, or central and western China + North America + Mexico. The North Atlantic and/or the Bering land bridges may be important in the widespread distribution across continents in the Northern Hemisphere. Our study highlights the importance of utilizing fossils in biogeographic inferences andusing data from different genomes while reconstructing deep and shallow phylogenies of organisms.

Past climate cooling and orogenesis of the Hengduan Mountains have influenced the evolution of Impatiens sect. Impatiens (Balsaminaceae) in the Northern Hemisphere

BackgroundImpatiens sect. Impatiens is distributed across the Northern Hemisphere and has diversified considerably, particularly within the Hengduan Mountains (HDM) in southwest China. Yet, the infra-sectional phylogenetic relationships are not well resolved, largely due to limited taxon sampling and an insufficient number of molecular markers. The evolutionary history of its diversification is also poorly understood. In this study, plastome data and the most complete sampling to date were used to reconstruct a robust phylogenetic framework for this section. The phylogeny was then used to investigate its biogeographical history and diversification patterns, specifically with the aim of understanding the role played by the HDM and past climatic changes in its diversification.ResultsA stable phylogeny was reconstructed that strongly supported both the monophyly of the section and its division into seven major clades (Clades I-VII). Molecular dating and ancestral area reconstruction suggest that sect. Impatiens originated in the HDM and Southeast China around 11.76 Ma, after which different lineages dispersed to Northwest China, temperate Eurasia, and North America, mainly during the Pliocene and Pleistocene. An intercontinental dispersal event from East Asia to western North America may have occurred via the Bering Land Bridge or Aleutian Islands. The diversification rate was high during its early history, especially with the HDM, but gradually decreased over time both within and outside the HDM. Multiple linear regression analysis showed that the distribution pattern of species richness was strongly associated with elevation range, elevation, and mean annual temperature. Finally, ancestral niche analysis indicated that sect. Impatiens originated in a relatively cool, middle-elevation area.ConclusionsWe inferred the evolutionary history of sect. Impatiens based on a solid phylogenetic framework. The HDM was the primary source or pump of its diversity in the Northern Hemisphere. Orogeny and climate change may have also shaped its diversification rates, as a steady decrease in the diversification rate coincided with the uplift of the HDM and climate cooling. These findings provide insights into the distribution pattern of sect. Impatiens and other plants in the Northern Hemisphere.

Molecular phylogeny, biogeography, and species delimitation of segmented spider genus Liphistius (Araneae: Liphistiidae) in Thailand

Abstract Mesothelae, or primitively segmented trapdoor spiders, form the most basal clade among living spiders. In Southeast Asia, Liphistius is the only genus recognized in the extant family Liphistiidae. Liphistius taxonomy and species identification are based largely on characters of the genitalia; however, the female genitalia show high intraspecific variation, males are rarely collected, and the phylogenetic relationships among the 69 described Liphistius species are unresolved. Here, we focused on the Liphistius of Thailand, including 37 described and numerous undescribed species in four species groups. We generated sequences from five loci (COI, 16S, H3, 28S, and ITS2) for 162 specimens from 52 sites in Thailand and Myanmar to reconstruct phylogenetic relationships, infer historical biogeography, and delimit species. The five-locus data set resolved nearly all species and species group relationships and was mostly congruent with morphology-based classifications. Ancestral area reconstruction suggested that Liphistius originated in Sibumasu (Siam–Burma–Malaysia–Sumatra) and diversified into several species groups, four (birmanicus, bristowei, linang, and trang) of which are found in Thailand. Speciation within Liphistius occurred in the area corresponding to their current distribution. All delimitation methods tested (ASAP, GMYC, PTP, STACEY and BFD) delimited specimens from discrete locations as separate species; variation in the number of species proposed (ranging from 53 to 72) stemmed from variation in delimitation of sympatric cryptic species.

Origins of cryophilous lineages and the role of Beringia: evidence from the cosmopolitan angiosperm genus Stellaria L. (Caryophyllaceae)

Abstract The cosmopolitan angiosperm genus Stellaria L. (Caryophyllaceae) occurs across the Arctic and is most diverse in the high southern Asian mountains, including presence at the most extreme latitudinal and elevational limits of vascular plants. Using the primary fossil record and double digest restriction site-associated DNA sequencing data, we estimated divergence times of Stellaria and relatives across the Caryophyllaceae. We then used ancestral area and ancestral state reconstructions to interpret the biogeographical history of the group. We found that Stellaria originated in the Miocene and gave rise to repeated New World lineages, mostly from temperate Old World regions and probably via Bering Land Bridges. Circumboreal lineages were recovered of recent, Pleistocene origin and several might have originated in southerly mountains of both the Old World and the New World before subsequently colonizing the Arctic. Ancestral state reconstruction of inhabitance of cold vs. temperate climates and of wet vs. dry habitats revealed repeated evolutionary transitions across these extremes by members of the genus worldwide. Our study, which samples nearly all species within a diverse and cosmopolitan lineage of flowering plants, recovers a group characterized by niche lability and helps to support prior findings of temperate origins of many cryophilous plant lineages. Pre-adaptation to cold might have been a prerequisite for colonization of the Arctic.

Molecular phylogenetics and biogeography reveal the origin of cherries (Prunus subg. Cerasus, Rosaceae)

Abstract Cherries (subg. Cerasus) belong to Prunus s.l. (Rosaceae) and are widely distributed in temperate and subtropical regions of the Northern Hemisphere. Given its ornamental and edible functions, it is a hugely preferred germplasm resource for human societies. However, the interspecific phylogenetic relationships, divergence times, and routes of this subgenus remain unclear. To reveal its enigmatic and intricate evolutionary history, we newly sequenced 12 subg. Cerasus species, reconstructed the plastome phylogeny with 24 previously published subg. Cerasus species. This study supports that subg. Cerasus split into five clades, among which P. mahaleb is the basal group of subg. Cerasus; P. campanulata is genetically distantly related to P. cerasoides and is not recommended for treatment as a variety of the latter; P. subhirtella is involved in the speciation of P. yedoensis. Molecular dating and ancestral area reconstructions infer that subg. Cerasus originated in the Eastern Mediterranean–Central Asia before 11.57 Mya (95% HPD = 5.34–19.1 Mya) and subsequently spread into the Qinghai-Tibetan Plateau (QTP) and adjacent regions. The first dispersal event of modern subg. Cerasus was facilitated by ‘out-of-QTP’, colonizing North America across the Bering Land Bridge and re-dispersing into Europe from the Late Miocene to Pliocene and forming the initial distribution pattern of extant subg. Cerasus in the Pliocene; The end of the Quaternary glacial period witnessed a second dispersal event, and core subg. Cerasus population diversity flourished radially in its separate refugia during the Late Pleistocene.

New insights into infrageneric relationships of Lonicera (Caprifoliaceae) as revealed by nuclear ribosomal DNA cistron data and plastid phylogenomics

AbstractThe discontinuous geographic distribution pattern of plants in the north temperate zone has been a focus of biogeographic research, especially concerning the mechanisms behind the formation of such a pattern and the spatial and temporal evolution of this intermittent distribution pattern. Hypotheses of boreotropical origin, land bridge migration, and out‐of‐Tibet have been proposed to explain the formation of the discontinuous distribution pattern. The distribution of Lonicera shows a typical Europe–Asia–North America discontinuous distribution, which makes for a good case study to investigate the above three hypotheses. In this study, we inferred the phylogeny based on plastid genomes and a nuclear data set with broad taxon sampling, covering 83 species representing two subgenera and four sections. Both nuclear and plastid phylogenetic analyses found section Isika polyphyletic, while sections Nintooa, Isoxylosteum, and Coelxylosteum were monophyletic in subgenus Chamaecerasus. Based on the nuclear and chloroplast phylogeny, we suggest transferring Lonicera maximowiczii and Lonicera tangutica into section Nintooa. Reconstruction of ancestral areas suggests that Lonicera originated in the Qinghai–Tibetan Plateau (QTP) and/or Asia, and subsequently dispersed to other regions. The aridification of the Asian interior may have facilitated the rapid radiation of Lonicera in the region. At the same time, the uplifts of the Tibetan Plateau appear to have triggered the spread and recent rapid diversification of the genus on the QTP and adjacent areas. Overall, our results deepen the understanding of the evolutionary diversification history of Lonicera.

Understanding the diversification and functional radiation of Aporrectodea (Crassiclitellata, Lumbricidae) through molecular phylogenetics of its endemic species

The genus Aporrectodea includes some of the most conspicuous earthworm species, but its taxonomic history is among the most complex within the family Lumbricidae. Molecular phylogenetic studies have produced some advances by assigning former Aporrectodea species to other monophyletic clades and by detecting species level lineages within the cosmopolitan caliginosa-trapezoides complex. However, little attention has been devoted to endemic taxa of Aporrectodea such as Ap. rubra, Ap. arverna, Ap. gogna, Ap. balisa, Ap. velox, Ap. giardi voconca and Ap. longa ripicola. These earthworms (and additional populations of Ap. longa and Ap. nocturna) were included in a molecular phylogenetic framework in order to reconstruct the ancestral range of the genus, as well as to help understand its diversification within its native range and to perform a systematic revision. Species delimitation, ancestral area reconstruction and Bayesian inference of the phylogenetic relationships were performed using a large gene sequence (COI) dataset and a narrower dataset composed of 5 mitochondrial and nuclear markers. Phylogenetic position and species delimitation indicated that Ap. giardi voconca and Ap. longa ripicola constitute species-level entities not closely related to Ap. giardi or Ap. longa, and they were thus redescribed as Aporrectodea voconca stat. nov. and Aporrectodea ripicola stat. nov. Ancestral area reconstruction enabled location of the origin of Aporrectodea in the Auvergne-Rhône-Alps, in Southeastern France. The study findings provide some insight into the evolution of functional traits in this ecologically successful genus. Ap. rubra and Ap. arverna (small, reddish, epigeic/epianecic) and Ap. gogna (very large, dark, anecic) were recovered as the earliest branching taxa, suggesting a complex evolution of functional traits within this genus.

Unity in diversity: morphological and genetic variability, integrative systematics, and phylogeography of the widespread nudibranch mollusc Onchidoris muricata

Onchidoris muricata (Gastropoda: Nudibranchia: Onchidorididae) is a well-known nudibranch species, which has a wide amphiboreal range confirmed by molecular data. However, O. muricata shows a high degree of variation in external morphology among distant populations, which may indicate the presence of cryptic diversity within this species. There are also two closely related species with an unconfirmed taxonomic status, which were recently described from the northwestern Pacific based on morphological data. In this paper we study the taxonomic status and population structure of O. muricata based on an integrative approach combining morphological and molecular data and using O. muricata as a model we explore issues of boreal marine fauna connectivity and glaciation-driven isolation. The external morphology, spicule composition, and features of the buccal armature and the reproductive system were studied using light microscopy, scanning electron microscopy and mCT scan technology. The molecular study included various population genetic analyses as well as divergence time estimation and ancestral area reconstruction analyses. Onchidoris muricata represents a true amphiboreal species, which shows a high degree of heterogeneity in morphological characters, especially in the radular morphology and in features of the reproductive system. Our new data question the validity of the North-West Pacific species O. macropompa and O. pavli as the morphology of both these species fall within the phenotypic diversity of O. muricata. Although our sampling does not include the type localities of these two species, the observed morphological variability in O. muricata and the lack of molecular data for the North Pacific species O. macropompa and O. pavli suggest the latter two species are in fact part of O. muricata morphological diversity. Phylogeographic analyses indicate a genetic separation of the North Pacific and North Atlantic-Arctic populations of O. muricata, suggesting restricted gene flow between these areas. We show that this divergence may be a result of glacial cycles during the late Pleistocene, which were a key factor in the reduction of gene flow across the Arctic Ocean. Our molecular results also suggest that the White Sea population experienced a bottleneck event during the last Glacial Maximum.

Plastome phylogenomics reveals an early Pliocene North- and Central America colonization by long-distance dispersal from South America of a highly diverse bromeliad lineage.

Understanding the spatial and temporal frameworks of species diversification is fundamental in evolutionary biology. Assessing the geographic origin and dispersal history of highly diverse lineages of rapid diversification can be hindered by the lack of appropriately sampled, resolved, and strongly supported phylogenetic contexts. The use of currently available cost-efficient sequencing strategies allows for the generation of a substantial amount of sequence data for dense taxonomic samplings, which together with well-curated geographic information and biogeographic models allow us to formally test the mode and tempo of dispersal events occurring in quick succession. Here, we assess the spatial and temporal frameworks for the origin and dispersal history of the expanded clade K, a highly diverse Tillandsia subgenus Tillandsia (Bromeliaceae, Poales) lineage hypothesized to have undergone a rapid radiation across the Neotropics. We assembled full plastomes from Hyb-Seq data for a dense taxon sampling of the expanded clade K plus a careful selection of outgroup species and used them to estimate a time- calibrated phylogenetic framework. This dated phylogenetic hypothesis was then used to perform biogeographic model tests and ancestral area reconstructions based on a comprehensive compilation of geographic information. The expanded clade K colonized North and Central America, specifically the Mexican transition zone and the Mesoamerican dominion, by long-distance dispersal from South America at least 4.86 Mya, when most of the Mexican highlands were already formed. Several dispersal events occurred subsequently northward to the southern Nearctic region, eastward to the Caribbean, and southward to the Pacific dominion during the last 2.8 Mya, a period characterized by pronounced climate fluctuations, derived from glacial-interglacial climate oscillations, and substantial volcanic activity, mainly in the Trans-Mexican Volcanic Belt. Our taxon sampling design allowed us to calibrate for the first time several nodes, not only within the expanded clade K focal group but also in other Tillandsioideae lineages. We expect that this dated phylogenetic framework will facilitate future macroevolutionary studies and provide reference age estimates to perform secondary calibrations for other Tillandsioideae lineages.