Ancestral Area Analysis Research Articles

Ancestral area analyses reveal Pleistocene‐influenced evolution in a clade of coastal plain endemic plants

AbstractAimThe North American Coastal Plain is currently recognized as a global biodiversity hotspot. However, the mechanisms driving high levels of species richness in a region with relatively low topographic relief and homogeneous climate are unclear. We investigated the evolutionary processes driving ancestral area evolution and diversification in a biodiversity hotspot from both a systematic and biogeographical context using a clade endemic to the hotspot.LocationNorth American Coastal Plain.TaxonThe Scrub Mint clade (SMC) comprises Dicerandra, Conradina, Piloblephis, Stachydeoma and four species of Clinopodium (Mentheae; Lamiaceae), almost all of which are endemic to the North American Coastal Plain.MethodsWe generated a dated phylogeny using a target enrichment/capture dataset and then calculated ancestral area using biogeographical models. We uncovered neo‐ and palaeo‐endemism hotspots and inferred ancestral potential ranges at each node based on ancestral niche reconstructions and palaeoclimatic data to understand the geographical range evolution of subclades.ResultsAncestral area for the SMC was inferred to be the Florida Panhandle/Apalachicola River basin. A diversification event likely happened around the mid‐Pleistocene Transition. Endemism hotspots were recovered in NE Florida, the Atlantic Coastal Ridge, and along the Lake Wales Ridge. Reconstructions of potential ranges support biogeographical findings, with the ancestor of the SMC likely located in the vicinity of the northeastern Gulf Coast during interglacial and glacial periods.Main ConclusionsThe timing of diversification events and colonization of new areas by ancestors of the SMC are consistent with the timing of major geological events in the region. The presence of multiple types of endemism highlights the complexity of evolutionary and ecological processes that foster the large number of endemic taxa found in this region. Efforts to identify hotspots in this region will be critical to preserving the remaining pockets of biodiversity threatened by global change.

Reconstructing an historical pollination syndrome: keel flowers

BackgroundKeel flowers are bilaterally symmetrical, pentamerous flowers with three different petal types and reproductive organs enclosed by keel petals; generally there is also connation of floral parts such as stamens and keel petals. In this study, the evolution of keel flowers within the order Fabales is explored to investigate whether the establishment of this flower type within one of the species-rich families, the Fabaceae (Leguminosae), preceded and could have influenced the evolution of keel flowers in the Polygalaceae. We conducted molecular dating, and ancestral area and ancestral state analyses for a phylogeny constructed for 678 taxa using published matK, rbcL and trnL plastid gene regions.ResultsWe reveal the temporal and spatial origins of keel flowers and traits associated with pollinators, specifically floral symmetry, the presence or absence of a pentamerous corolla and three distinct petal types, the presence or absence of enclosed reproductive organs, androecium types, inflorescence types, inflorescence size, flower size, plant height and habit. Ancestral area reconstructions show that at the time keel flowers appeared in the Polygaleae, subfamily Papilionoideae of the Fabaceae was already distributed almost globally; at least eight clades of the Papilionoideae had keel flowers with a functional morphology broadly similar to the morphology of the first evolving Polygaleae flowers.ConclusionsThe multiple origins of keel flowers within angiosperms likely represent convergence due to bee specialization, and therefore pollinator pressure. In the case of the Fabales, the first evolving keel flowers of Polygaleae have a functional morphology that corresponds with keel flowers of species of the Papilionoideae already present in the environment. These findings are consistent with the keel-flowered Polygaleae exploiting pollinators of keel-flowered Papilionoideae. The current study is the first to use ancestral reconstructions of traits associated with pollination to demonstrate that the multiple evolutionary origins of the keel flower pollinator syndrome in Fabales are consistent with, though do not prove, mimicry.

An integrative taxonomic revision of slug-eating snakes (Squamata: Pareidae: Pareineae) reveals unprecedented diversity in Indochina.

Slug-eating snakes of the subfamily Pareinae are an insufficiently studied group of snakes specialized in feeding on terrestrial mollusks. Currently Pareinae encompass three genera with 34 species distributed across the Oriental biogeographic region. Despite the recent significant progress in understanding of Pareinae diversity, the subfamily remains taxonomically challenging. Here we present an updated phylogeny of the subfamily with a comprehensive taxon sampling including 30 currently recognized Pareinae species and several previously unknown candidate species and lineages. Phylogenetic analyses of mtDNA and nuDNA data supported the monophyly of the three genera Asthenodipsas, Aplopeltura, and Pareas. Within both Asthenodipsas and Pareas our analyses recovered deep differentiation with each genus being represented by two morphologically diagnosable clades, which we treat as subgenera. We further apply an integrative taxonomic approach, including analyses of molecular and morphological data, along with examination of available type materials, to address the longstanding taxonomic questions of the subgenus Pareas, and reveal the high level of hidden diversity of these snakes in Indochina. We restrict the distribution of P. carinatus to southern Southeast Asia, and recognize two subspecies within it, including one new subspecies proposed for the populations from Thailand and Myanmar. We further revalidate P. berdmorei, synonymize P. menglaensis with P. berdmorei, and recognize three subspecies within this taxon, including the new subspecies erected for the populations from Laos and Vietnam. Furthermore, we describe two new species of Pareas from Vietnam: one belonging to the P. carinatus group from southern Vietnam, and a new member of the P. nuchalis group from the central Vietnam. We provide new data on P. temporalis, and report on a significant range extension for P. nuchalis. Our phylogeny, along with molecular clock and ancestral area analyses, reveal a complex diversification pattern of Pareinae involving a high degree of sympatry of widespread and endemic species. Our analyses support the “upstream” colonization hypothesis and, thus, the Pareinae appears to have originated in Sundaland during the middle Eocene and then colonized mainland Asia in early Oligocene. Sundaland and Eastern Indochina appear to have played the key roles as the centers of Pareinae diversification. Our results reveal that both vicariance and dispersal are responsible for current distribution patterns of Pareinae, with tectonic movements, orogeny and paleoclimatic shifts being the probable drivers of diversification. Our study brings the total number of Pareidae species to 41 and further highlights the importance of comprehensive taxonomic revisions not only for the better understanding of biodiversity and its evolution, but also for the elaboration of adequate conservation actions.

Collections‐based systematics and biogeography in the 21st century: A tribute to Dr. Vicki Funk

Collections‐based systematics and biogeography in the 21st century: A tribute to Dr. Vicki Funk

A little frog leaps a long way: compounded colonizations of the Indian Subcontinent discovered in the tiny Oriental frog genus Microhyla (Amphibia: Microhylidae).

Frogs of the genus Microhyla include some of the world’s smallest amphibians and represent the largest radiation of Asian microhylids, currently encompassing 50 species, distributed across the Oriental biogeographic region. The genus Microhyla remains one of the taxonomically most challenging groups of Asian frogs and was found to be paraphyletic with respect to large-sized fossorial Glyphoglossus. In this study we present a time-calibrated phylogeny for frogs in the genus Microhyla, and discuss taxonomy, historical biogeography, and morphological evolution of these frogs. Our updated phylogeny of the genus with nearly complete taxon sampling includes 48 nominal Microhyla species and several undescribed candidate species. Phylogenetic analyses of 3,207 bp of combined mtDNA and nuDNA data recovered three well-supported groups: the Glyphoglossus clade, Southeast Asian Microhyla II clade (includes M. annectens species group), and a diverse Microhyla I clade including all other species. Within the largest major clade of Microhyla are seven well-supported subclades that we identify as the M. achatina, M. fissipes, M. berdmorei, M. superciliaris, M. ornata, M. butleri, and M. palmipes species groups. The phylogenetic position of 12 poorly known Microhyla species is clarified for the first time. These phylogenetic results, along with molecular clock and ancestral area analyses, show the Microhyla—Glyphoglossus assemblage to have originated in Southeast Asia in the middle Eocene just after the first hypothesized land connections between the Indian Plate and the Asian mainland. While Glyphoglossus and Microhyla II remained within their ancestral ranges, Microhyla I expanded its distribution generally east to west, colonizing and diversifying through the Cenozoic. The Indian Subcontinent was colonized by members of five Microhyla species groups independently, starting with the end Oligocene—early Miocene that coincides with an onset of seasonally dry climates in South Asia. Body size evolution modeling suggests that four groups of Microhyla have independently achieved extreme miniaturization with adult body size below 15 mm. Three of the five smallest Microhyla species are obligate phytotelm-breeders and we argue that their peculiar reproductive biology may be a factor involved in miniaturization. Body size increases in Microhyla—Glyphoglossus seem to be associated with a burrowing adaptation to seasonally dry habitats. Species delimitation analyses suggest a vast underestimation of species richness and diversity in Microhyla and reveal 15–33 undescribed species. We revalidate M. nepenthicola, synonymize M. pulverata with M. marmorata, and provide insights on taxonomic statuses of a number of poorly known species. Further integrative studies, combining evidence from phylogeny, morphology, advertisement calls, and behavior will result in a better systematic understanding of this morphologically cryptic radiation of Asian frogs.

Biogeographic history and diversification patterns in the Irano-Turanian genus Acanthophyllum s.l. (Caryophyllaceae)

The Irano-Turanian (IT) floristic region in Asia contains three biodiversity hotspots and has been a source of xerophytic taxa for neighboring regions. Despite its species richness and large territory, the evolutionary history and biogeography of this floristic region is poorly understood. Acanthophyllum, encompassing ca. 70 subshrubby mostly thorny-cushion species, is one of the important components of the steppe and mountain vegetation of this region. In this study, we investigate the tempo and mode of diversification as well as the biogeographic patterns of this genus. The ancestral area analysis suggests that Acanthophyllum originated east of the Zagros Mountains in the Miocene, from where it expanded westwards. A shift in the speciation rate in the late Pliocene (ca. 3.24 Ma) was detected, based on a nrDNA ITS tree, affecting the lineage of the largest section in the genus, Acanthophyllym sect. Oligosperma. Parallelisms with another IT species-rich genera in aspects such as largely coincident ranges and habitats, presence of a thorny-cushion life-form, similar areas reconstructed for their MRCA, and the inference of a shift in speciation in the region suggest common underlying abiotic and biotic factors or even drivers for diversification and speciation in the high elevation dry continental landscape of IT region.

Phylogeny, biogeography, and morphological ancestral character reconstruction in the Mediterranean genus Fumana (Cistaceae)

AbstractFumana is a diverse genus of the Cistaceae family, consisting of 21 currently accepted species. In this study, nuclear (ITS) and plastid (matK, trnT‐L) molecular markers were used to reconstruct the phylogeny and to estimate divergence times, including 19 species of Fumana. Phylogenetic analyses (Bayesian Inference, Maximum Parsimony and Maximum Likelihood) confirmed the monophyly of Fumana and did not support the infrageneric divisions previously established. The results support four main clades that group species that differ in vegetative and reproductive characters. Given the impossibility to define morphological characters common to all species within the clades, our proposal is to reject infrageneric divisions. Molecular dating and ancestral area analyses provide evidence for a Miocene diversification of the genus in the north‐western Mediterranean. Ancestral state reconstructions revealed ancestral character states for some traits related to xeric and arid habitats, suggesting a preadaptation to the Mediterranean climate.

Phylogenetic relationships and biogeographic history of the unique Saxifraga sect. Irregulares (Saxifragaceae) from eastern Asia

AbstractSaxifraga L. is the largest genus in Saxifragaceae and a characteristic component of the herbaceous flora of the temperate and alpine mountains in the Northern Hemisphere. Section Irregulares is a small group of 15–20 species, representing one of the early‐diverged lineages in the genus characterized with unique zygomorphic flowers. We used both nuclear internal transcribed spacer and chloroplast DNA regions (psbA‐trnH, trnL‐F, and matK) to reconstruct its species relationships, estimate divergence times, and infer its historical biogeography. Our phylogenetic results corroborate the monophyly of sect. Irregulares and its sister relationship to sect. Heterisia from North America. The section was well resolved into two lineages corresponding to their morphological features and biogeographic distributions. One represents ser. Stoloniferae including S. stolonifera Curtis and S. nipponica Makino with long‐creeping stolons/rhizomes and small petals with spots and the other comprises the remaining taxa (ser. Rufescentes) which lack long‐creeping rhizomes. Spots on leaves (abaxially spotted vs. abaxially without spots) and spots on petals (without spots vs. with spots) are inferred to be phylogenetically informative within ser. Rufescentes. Divergence time estimates and ancestral area analysis suggested a western North American origin of sect. Irregulares with migration into East Asia by way of the Bering land bridge in the Middle Oligocene. The development of drying and desertification belt in the late Miocene could have played an important role in the subsequent restriction and separation of the north and south lineages within eastern Asia.

Global phylogeography reveals the origin and the evolutionary history of the gypsy moth (Lepidoptera, Erebidae)

We examined the global phylogeography of gypsy moth (Lymantria dispar L.) using molecular data based on mitochondrial and nuclear genes. Populations from all biogeographic regions of the native and introduced range of L. dispar, were sampled to fully document intraspecific and subspecies variation, identify potential cryptic species, and to clarify the relationships among major phylogeographic lineages. We recovered three major mtDNA lineages of L. dispar: Transcaucasia; East Asia + Japan; and Europe + Central Asia. The circumscription of these lineages is only partially consistent with the current taxonomic concept (i.e., L. dispar dispar; L. dispar asiatica; L. dispar japonica), with the following important discrepancies: (1) north-central Asian populations, including topotypical populations of L. dispar asiatica, may be more closely related to European rather than Asian segregates, which would require the synonymization of the taxon asiatica and establishment of a new name; (2) the Japanese populations (L. d. japonica) are not distinct from east Asian populations; (3) the presence of a distinct, unnamed mitogenomic lineage endemic to the Trancaucasus region. We demonstrated that the population from Transcaucasia contains the highest mitochondrial haplotype diversity among L. dispar, potentially indicative of an ancestral area for the entire dispar-group. Our study corroborates the endemic Hokkaido, Japan taxon Lymantria umbrosa (Butler) as the sister group to all other L. dispar populations, but the applicability of the names umbrosa versus hokkaidoensis Goldschmidt needs to be re-evaluated. The ancestral area analysis suggest that Japan was likely colonized via Sakhalin ∼1 Mya, in contrast to previous studies which have suggested colonization of the Japanese archipelago via the Korean Peninsula. Lastly, mitogenomic variation within L. dispar is incongruent with phylogenies based on nuclear DNA, as nDNA gene phylogenies did not recover the three major mtDNA lineages, and also failed to recover L. dispar and L. umbrosa as reciprocally monophyletic.

Historical Biogeography of Melanthiaceae: A Case of Out-of-North America Through the Bering Land Bridge.

Intercontinental floristic disjunction between East Asia and North America in the Northern Hemisphere has received much attention during the past decades, but few studies have focused on the family level. Melanthiaceae, containing 196 species and 17 genera circumscribed in five tribes, is disjunctly distributed in Eurasia and North America. It is one of the foremost models for studying the evolution of biogeographic patterns in this region. Here, we present a fossil-calibrated, molecular phylogeny of Melanthiaceae based on two chloroplast DNA datasets: one dataset includes extensive sampling (94 species representing all 17 genera of Melanthiaceae) of four chloroplast DNA regions (atpB, rbcL, matK, and ndhF) and the other includes six species representing all tribes of the family for 78 coding genes of the chloroplast genome. Within this framework, we infer the historical biogeography of Melanthiaceae. Both datasets produce well-resolved phylogenies of Melanthiaceae showing the monophyly of the family and the relationships among the five tribes. Melanthieae is found to be sister to the rest of the tribes of the family and the remaining taxa are divided into two major clades consisting of the Chionographideae + Heloniadeae clade and the Parideae + Xerophylleae clade. The molecular dating and the ancestral area analyses suggest that Melanthiaceae most likely originated in North America with its crown group dated at 92.1 mya in the late Cretaceous. The favored ancestral areas at the crown lineages of tribes are also in North America. In the family, seven independent migrations into East Asia from North America are inferred to have occurred in the Oligocene and the Miocene-Pliocene via historical paleo-land bridge connections. Cooling trends during the Oligocene resulted in the present East Asia-North America disjunct distribution, while the warm period during the middle Miocene and habitat heterogeneity stimulated diversification in East Asia. Our study provides the phylogenetic and biogeographical history of the Melanthiaceae and adds an example of “out of North America” migration in the biogeographic history of the Northern Hemisphere.

Genotyping-by-sequencing (GBS), ITS and cpDNA phylogenies reveal the existence of a distinct Pyrenean/Cantabrian lineage in the European high mountain genus Homogyne (Asteraceae) and imply dual westward migration of the genus

Quaternary climatic oscillations have been a major factor in shaping plant diversity and distribution in the European Alpine System (EAS). Plants responded to these oscillations with repeated changes in their abundance and geographical distribution. However, oscillating shifts in geographical distribution have only rarely been reported in molecular analyses of genetic variation across the EAS. Homogyne, a genus endemic to the EAS, contains three species. While H. discolor and H. sylvestris are confined to the periphery of the Eastern Alps, H. alpina is widespread across the EAS. In phylogenetic reconstructions of a broad sample of Homogyne using DNA sequence data sets of the nuclear ribosomal internal transcribed spacer (ITS), plastid DNA (ndhF-rpl32, rpl32-trnL, psbA-trnH) and genotyping-by-sequencing (GBS), accessions of H. alpina from the Pyrenees and the Cantabrian Mts. form a clade which groups in conflicting positions. While the exact relationship of this Pyrenean/Cantabrian clade of H. alpina remains unclear, our data clearly imply that this clade is a lineage distinct from the remaining accessions of H. alpina (H. alpina s.str.). An ancestral area analysis unambiguously revealed the Eastern Alps as the ancestral area of the genus. Considering that relationships within H. alpina s.str. clearly illustrate East to West expansion, the identification of a Pyrenean/Cantabrian clade implies that westward expansion from an ancestral area in the Eastern Alps took place twice in the genus. Although the extant distributions of the Pyrenean/Cantabrian clade and H. alpina s.str. are mutually exclusive, plastid DNA evidence may imply past contact and hybridization between the two clades.

Phylogeny, biogeography, systematics and taxonomy of Salicornioideae (Amaranthaceae/Chenopodiaceae) – A cosmopolitan, highly specialized hygrohalophyte lineage dating back to the Oligocene

AbstractSalicornioideae (Amaranthaceae / Chenopodiaceae) comprise 11 genera and ca. 100 species of succulent halophytes distributed worldwide in coastal and inland saline habitats. Most species have peculiar articulated, seemingly leafless stems and spike‐like sessile thyrses with highly reduced flowers hidden by fleshy bracts. We analysed sequence data of four markers (ETS, ITS, atpB‐rbcL, matK‐trnK) from 57 species, 9 subspecies, 1 variety and 2 hybrids representing all curently accepted genera using maximum likelihood, Bayesian analysis, fossil‐calibrated molecular dating and ancestral area analysis. All molecular markers gave similar phylogenetic signals. Salicornioideae probably originated in Eurasia during the late Eocene–early Oligocene. The divergence of the early main clades took place in the middle Oligocene with the separation of Allenrolfea /Heterostachys, Halocnemum /Halopeplis /Halostachys /Kalidium and Arthrocnemum /Microcnemum /Tecticornia /Salicornia/ Sarcocornia lineages. The latter lineage diversified most and comprises ¾ of the species of the subfamily. The Arthrocnemum macrostachyum /Microcnemum lineage diverged at the turn of the Oligocene/Miocene – while the Arthrocnemum subterminale, Tecticornia and Salicornia /Sarcocornia lineages were all present by the middle Miocene. Long‐distance dispersal has taken place several times to the Americas (Allenrolfea /Heterostachys, Arthrocnemum subterminale, Salicornia /Sarcocornia), South Africa (Halopeplis, Salicornia /Sarcocornia) and Australia (Tecticornia, Salicornia /Sarcocornia). Most currently accepted genera were resolved as monophyletic. However, Sarcocornia is paraphyletic in relation to Salicornia, and Arthrocnemum proved to be polyphyletic. In addition, the name Arthrocnemum is a nomenclatural synonym of Salicornia. As a consequence, we propose the merging of Sarcocornia under Salicornia and provide 19 new nomenclatural combinations and one replacement name. For Salicornia (incl. Sarcocornia) we propose a new infrageneric classification to accommodate the four phylogenetically and geographically well‐supported sublineages of the genus. We also propose abandoning the name Arthrocnemum in its current use, and describe two new genera, Arthrocaulon (Eurasia, Africa) and Arthroceras (North America), and provide three new nomenclatural combinations.

The evolutionary history of Eugenia sect. Phyllocalyx (Myrtaceae) corroborates historically stable areas in the southern Atlantic forests.

Eugenia sect. Phyllocalyx Nied. includes 14 species endemic to the Neotropics, mostly distributed in the Atlantic coastal forests of Brazil. Here the first comprehensive phylogenetic study of this group is presented, and this phylogeny is used as the basis to evaluate the recent infrageneric classification in Eugenia sensu lato (s.l.) to test the history of the evolution of traits in the group and test hypotheses associated with the history of this clade. A total of 42 taxa were sampled, of which 14 were Eugenia sect. Phyllocalyx for one nuclear (ribosomal internal transcribed spacer) and four plastid markers (psbA-trnH, rpl16, trnL-rpl32 and trnQ-rps16). The relationships were reconstructed based on Bayesian analysis and maximum likelihood. Additionally, ancestral area analysis and modelling methods were used to estimate species dispersal, comparing historically climatic stable (refuges) and unstable areas. Maximum likelihood and Bayesian inferences indicate that Eugenia sect. Phyllocalyx is paraphyletic and the two clades recovered are characterized by combinations of morphological characters. Phylogenetic relationships support a link between Cerrado and south-eastern species and a difference in the composition of species from north-eastern and south-eastern Atlantic forest. Refugia and stable areas identified within unstable areas suggest that these areas were important to maintain diversity in the Atlantic forest biodiversity hotspot. This study provides a robust phylogenetic framework to address important historical questions for Eugenia s.l. within an evolutionary context, supporting the need for better taxonomic study of one of the largest genera in the Neotropics. Furthermore, valuable insight is offered into diversification and biome shifts of plant species in the highly environmentally impacted Atlantic forest of South America. Evidence is presented that climate stability in the south-eastern Atlantic forest during the Quaternary contributed to the highest levels of plant diversity in this region that acted as a refugium.

A tale of North and South America: time and mode of dispersal of the amphitropical genusMunroa(Poaceae, Chloridoideae)

Plant disjunctions have provided some of the most intriguing distribution patterns historically addressed by biogeographers. We evaluated the three hypotheses that have been postulated to explain these patterns [vicariance, stepping-stone dispersal and long-distance dispersal (LDD)] using Munroa, an American genus of grasses with six species and a disjunct distribution between the desert regions of North and South America. The ages of clades, cytology, ancestral characters and areas of distribution were investigated in order to establish relationships among species, to determine the time of divergence of the genus and its main lineages, and to understand further the biogeographical and evolutionary history of this genus. Bayesian inference recovered the North American M. pulchella as sister species to the rest. Molecular dating and ancestral area analyses suggest that Munroa originated in North America in the late Miocene–Pliocene (7.2 Mya; 8.2–6.5 Mya). Based on these results, we postulate that two dispersal events modelled the current distribution patterns of Munroa: the first from North to South America (7.2 Mya; 8.2–6.5 Mya) and the second (1.8 Mya; 2–0.8 Mya) from South to North America. Arid conditions of the late Miocene–Pliocene in the Neogene and Quaternary climatic oscillations in North America and South America were probably advantageous for the establishment of populations of Munroa. We did not find any relationship between ploidy and dispersal events, and our ancestral character analyses suggest that shifts associated with dispersal and seedling establishment, such as habit, reproductive system, disarticulation of rachilla, and shape and texture of the glume, have been important in these species reaching new areas. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179, 110–125.

North or south? Phylogenetic and biogeographic origins of a globally distributed avian clade

Establishing phylogenetic relationships within a clade can help to infer ancestral origins and indicate how widespread species reached their current biogeographic distributions. The small plovers, genus Charadrius, are cosmopolitan shorebirds, distributed across all continents except Antarctica. Here we present a global, species-level molecular phylogeny of this group based on four nuclear (ADH5, FIB7, MYO2 and RAG1) and two mitochondrial (COI and ND3) genes, and use the phylogeny to examine the biogeographic origin of the genus. A Bayesian multispecies coalescent approach identified two major clades (CRD I and CRD II) within the genus. Clade CRD I contains three species (Thinornis novaeseelandiae, Thinornis rubricollis and Eudromias morinellus), and CRD II one species (Anarhynchus frontalis), that were previously placed outside the Charadrius genus. In contrast to earlier work, ancestral area analyses using parsimony and Bayesian methods supported an origin of the Charadrius plovers in the Northern hemisphere. We propose that major radiations in this group were associated with shifts in the range of these ancestral plover species, leading to colonisation of the Southern hemisphere.

Phylogeny, taxonomy and biogeography of a circum-Indian Ocean clade of leaf-toed geckos (Reptilia: Gekkota), with a description of two new genera

Geckos with a leaf-toed morphology (digits with a single pair of enlarged adhesive pads located terminally) occur on six continents and many islands. Although most leaf-toed gecko genera belong to independently derived lineages, recent studies support the monophyly of a circum-Indian Ocean group including four genera from disparate regions: the southern African genera Afrogecko and Cryptactites, the Malagasy genus Matoatoa, and the Australian genus Christinus. We obtained molecular and/or morphological data for most species in these genera to estimate phylogenetic relationships among constituent species and infer broad historical biogeographic patterns. Our results confirm that Afrogecko is not monophyletic, and that Christinus is embedded among African taxa. Afrogecko is comprised of three lineages, each of which is distinct in external features and osteology. Based on these results, we partition Afrogecko and recognize two new genera. Molecular clock analyses suggest divergences within the circum-Indian Ocean group are too recent for Gondwanan vicariance or hypothesized land bridges (e.g. Kerguelen Plateau) to account for the observed Africa/Madagascar/Australia distributional pattern. Ancestral area analyses support an origin of the clade in mainland Africa or Madagascar, and imply a dispersal event from southern Africa to Australia, similar to those observed in some plant and arthropod taxa, but otherwise unknown among non-volant terrestrial vertebrates. Dispersal was likely via a southern route and may have been facilitated by island hopping using Antarctica or other southern landmasses available in the mid-Cainozoic.http://zoobank.org/urn:lsid:zoobank.org:pub:7706B624-CD49-45CC-9DA3-FAB370BEE12B).

Phylogeny and biogeography of tetralophodont rodents of the tribe Oryzomyini (Cricetidae: Sigmodontinae)

Oryzomyini is the richest tribe among the Sigmodontine rodents, encompassing 32 living and extinct genera and including an increasing number of recently described species and genera. Some Oryzomyini are tetralophodont showing a reduction in the number of molar folds to four, while most taxa in this tribe retain the plesiomorphic pentalophodont state. We applied phylogenetic methods, molecular dating techniques and ancestral area analyses to members of an oryzomyini clade informally named ‘D’ in former studies and included related fossil tetralophodont forms. Based on 98 morphological characters and sequences of five gene fragments, we found that the tetralophodont condition is paraphyletic. Among living taxa, Pseudoryzomys is sister to Holochilus, and Lundomys is derived from a basal divergence. A clade formed by living Holochilus and the fossils Noronhomys and Carletonomys is sister to Holochilus primigenus, making Holochilus paraphyletic. Therefore, we describe a new genus that accommodates the fossil H. primigenus. Because trans‐Andean taxa currently share a common ancestor with taxa of cis‐Adean distribution, the northern Andes uplift may have worked as a postdispersal barrier. The tetralophodont lineages diverged during the Pliocene from a cis‐Andean ancestor, and the Great Plains in South America may have favoured the diversification of tetralophodont forms adapted to open habitats during the Pliocene.

Geographical distribution and ecological diversification of South American octodontid rodents

AbstractCaviomorph rodents represent one of the most distinctive groups of mammals in southern South America drylands; they colonized South America from Africa via trans‐oceanic dispersions in the Eocene (40–50 Ma) and underwent an extraordinary ecological radiation after their arrival, thus making this group of great interest for biogeographic and evolutionary studies. The aim of this article was to provide a working hypothesis regarding the biogeographical history and ecological diversification of one of its conspicuous families, the Octodontidae. We reconstruct the evolutionary theater where their ecological diversification took place, and potential events of dispersal, vicariance and extinctions. We analyzed the historical biogeography of the Octodontidae across the eight ecoregions where they occur, based on species phylogeny and divergence times. Four approaches were used to reconstruct ancestral area: (1) Statistical Dispersal–Vicariance Snalysis (S‐DIVA); (2) Bayesian binary Markov chain Monte Carlo (MCMC) analysis implemented in Reconstruct Ancestral State in Phylogenies (RASP); (3) Fitch optimization method; and (d) weighted ancestral area analysis (WAAA). Parsimony ancestral state reconstructions were implemented in order to explore the evolutionary history of an ecological character, mode of life. We propose the northern portion of the Monte desert ecoregion as the ancestral area in the evolution of the Octodontidae, with subsequent dispersal and enlargement of the family geographic range. The evolution of their ecological specialization (i.e. modes of life) suggests an ambiguous ancestral condition (saxicolous, generalist terrestrial, semifossorial) linked to species adaptation to arid environments, with fossoriality appearing later in octodontid evolution. The evolution of the Octodontidae is associated with contrasting environmental conditions (i.e. climate and vegetation) produced by the Andean Uplift between eastern and western sides.

Phylogeny of bent-toed geckos (Cyrtodactylus) reveals a west to east pattern of diversification

The Asian/Pacific genus Cyrtodactylus is the most diverse and among the most widely distributed genera of geckos, and more species are continually being discovered. Major patterns in the evolutionary history of Cyrtodactylus have remained largely unknown because no published study has broadly sampled across the geographic range and morphological diversity of the genus. We assembled a data set including sequences from one mitochondrial and three nuclear loci for 68 Cyrtodactylus and 20 other gekkotan species to infer phylogenetic relationships within the genus and identify major biogeographic patterns. Our results indicate that Cyrtodactylus is monophyletic, but only if the Indian/Sri Lankan species sometimes recognized as Geckoella are included. Basal divergences divide Cyrtodactylus into three well-supported groups: the single species C. tibetanus, a clade of Myanmar/southern Himalayan species, and a large clade including all other Cyrtodactylus plus Geckoella. Within the largest major clade are several well-supported subclades, with separate subclades being most diverse in Thailand, Eastern Indochina, the Sunda region, the Papuan region, and the Philippines, respectively. The phylogenetic results, along with molecular clock and ancestral area analyses, show Cyrtodactylus to have originated in the circum-Himalayan region just after the Cretaceous/Paleogene boundary, with a generally west to east pattern of colonization and diversification progressing through the Cenozoic. Wallacean species are derived from within a Sundaland radiation, the Philippines were colonized from Borneo, and Australia was colonized twice, once via New Guinea and once via the Lesser Sundas. Overall, these results are consistent with past suggestions of a Palearctic origin for Cyrtodactylus, and highlight the key role of geography in diversification of the genus.

Dynamic colonization exchanges between continents and islands drive diversification in paradise‐flycatchers (Terpsiphone, Monarchidae)

AbstractAim We use parametric biogeographical reconstruction based on an extensive DNA sequence dataset to characterize the spatio‐temporal pattern of colonization of the Old World monarch flycatchers (Monarchidae). We then use this framework to examine the role of dispersal and colonization in their evolutionary diversification and to compare plumages between island and continentalTerpsiphonespecies.Location Africa, Asia and the Indian Ocean.Methods We generate a DNA sequence dataset of 2300 bp comprising one nuclear and three mitochondrial markers for 89% (17/19) of the Old World Monarchidae species and 70% of theTerpsiphonesubspecies. By applying maximum likelihood and Bayesian phylogenetic methods and implementing a Bayesian molecular clock to provide a temporal framework, we reveal the evolutionary history of the group. Furthermore, we employ both Lagrangeand Bayes‐Lagrangeanalyses to assess ancestral areas at each node of the phylogeny. By combining the ancestral area reconstruction with information on plumage traits we are able to compare patterns of plumage evolution on islands and continents.Results We provide the first comprehensive molecular phylogenetic reconstruction for the Old World Monarchidae. Our phylogenetic results reveal a relatively recent diversification associated with several dispersal events within this group. Moreover, ancestral area analyses reveal an Asian origin of the Indian Ocean and African clades. Ancestral state reconstruction analyses of plumage characters provide an interpretation of the plumage differentiation on islands and continents. Ancestral plumage traits are inferred to be close to those of the Asian paradise‐flycatcher (Terpsiphone paradisi), and island species display a high degree of plumage autapomorphy compared with continental species.Main conclusions Terpsiphone paradisiis polyphyletic and comprises populations that have retained the ancestral plumage of the widespreadTerpsiphonegenus. The genus appears to have colonized south‐west Asia, the Indian Ocean and Africa from eastern Asia. The phylogeny and divergence time estimates indicate multiple simultaneous colonizations of the western Old World byTerpsiphone. These results reinforce a hypothesis of range expansions of aTerpsiphone paradisi‐like ancestor into eastern Asia and the western Old World.