Phylogenetic relationships of the North American catfishes (Ictaluridae, Siluriformes): Investigating the origins and parallel evolution of the troglobitic species.

Insular habitats have played an important role in developing evolutionary theory, including natural selection and island biogeography. Caves are insular habitats that place extreme selective pressures on organisms due to the absence of light and food scarcity. Therefore, cave organisms present an excellent opportunity for studying colonization and speciation in response to the unique abiotic conditions that require extreme adaptations. One vertebrate family, the North American catfishes (Ictaluridae), includes four troglobitic species that inhabit the karst region bordering the western Gulf of Mexico. The phylogenetic relationships of these species have been contentious, and conflicting hypotheses have been proposed to explain their origins. The purpose of our study was to construct a time-calibrated phylogeny of Ictaluridae using first-occurrence fossil data and the largest molecular dataset on the group to date. We test the hypothesis that troglobitic ictalurids have evolved in parallel, thus resulting from repeated cave colonization events. We found that Prietella lundbergi is sister to surface-dwelling Ictalurus and that Prietella phreatophila + Trogloglanis pattersoni are sister to surface-dwelling Ameiurus, suggesting that ictalurids colonized subterranean habitats at least twice in evolutionary history. The sister relationship between Prietella phreatophila and Trogloglanis pattersoni may indicate that these two species diverged from a common ancestor following a subterranean dispersal event between Texas and Coahuila aquifers. We recovered Prietella as a polyphyletic genus and recommend P. lundbergi be removed from this genus. With respect to Ameiurus, we found evidence for a potentially undescribed species sister to A. platycephalus, which warrants further investigation of Atlantic and Gulf slope Ameiurus species. In Ictalurus, we identified shallow divergence between I. dugesii and I. ochoterenai, I. australis and I. mexicanus, and I. furcatus and I. meridionalis, indicating a need to reexamine the validity of each species. Lastly, we propose minor revisions to the intrageneric classification of Noturus including the restriction of subgenus Schilbeodes to N. gyrinus (type species), N. lachneri, N. leptacanthus, and N. nocturnus.

Following the aridity: Historical biogeography and diversification of the Philodromidae spider genus Petrichus in South America.

Aridity conditions and expansion of arid biomes in South America are closely linked to the onset of Andean orogeny since at least 30 Mya. Among arid-associated taxa, spiders belonging to the genus Petrichus are found along the Andes mountains and across the diagonal of open formations of the Chaco and Cerrado domains. In this contribution, we asked whether Petrichus originated prior to the central Andean uplift and what historical processes have promoted their diversification. We time-calibrated the phylogenetic tree of Philodromidae and estimated the divergence times of Petrichus. Considering phylogenetic uncertainty, we assessed biogeographical hypotheses of the historical events associated with the diversification of these spiders in South America. Petrichus originated along the Pacific coastal deserts in the Central Andes during the Early Miocene. The species likely dispersed from the western to the eastern side of the Andes coincidently with the central Andean uplift. The diversification of these spiders is coeval with the expansion of open grassland formations during the Late Miocene and Early Pliocene. Multiple dispersal events occurred from the Monte desert to southern South America and eastward to Chaco between âˆ¼ 8 and 2.5 Mya. The Andes might have played a role as a corridor favoring geographical range expansions and colonization of new environments. In addition, we also suggest that Philodromidae might have an Oligocene origin or earlier. Future analyses based on further evidence and larger taxon sampling should be carried out to corroborate our findings.

Deconstructing age estimates for angiosperms.

Estimates of the age of angiosperms from molecular phylogenies vary considerably. As in all estimates of evolutionary timescales from phylogenies, generating these estimates requires assumptions about the rate that molecular sequences are evolving (using clock models) and the time duration of the branches in a phylogeny (using fossil calibrations and branching processes). Often, it is difficult to demonstrate that these assumptions reflect current knowledge of molecular evolution or the fossil record. In this study we re-estimate the age of angiosperms using a minimal set of assumptions, therefore avoiding many of the assumptions inherent to other methods. The age estimates we generate are similar for each of the four datasets analysed, ranging from 130 to 400 Ma, but are far less precise than in previous studies. We demonstrate that this reduction in precision results from making less stringent assumptions about both rate and time, and that the analysed molecular dataset has very little effect on age estimates.

Genetic assimilation and the evolution of direction of genital asymmetry in anablepid fishes.

Phylogenetic comparative studies suggest that the direction of deviation from bilateral symmetry (sidedness) might evolve through genetic assimilation; however, the changes in sidedness inheritance remain largely unknown. We investigated the evolution of genital asymmetry in fish of the family Anablepidae, in which males' intromittent organ (the gonopodium, a modified anal fin) bends asymmetrically to the left or the right. In most species, males show a 1 : 1 ratio of left-to-right-sided gonopodia. However, we found that in three species left-sided males are significantly more abundant than right-sided ones. We mapped sidedness onto a new molecular phylogeny, finding that this left-sided bias likely evolved independently three times. Our breeding experiment in a species with an excess of left-sided males showed that sires produced more left-sided offspring independently of their own sidedness. We propose that sidedness might be inherited as a threshold trait, with different thresholds across species. This resolves the apparent paradox that, while there is evidence for the evolution of sidedness, commonly there is a lack of support for its heritability and no response to artificial selection. Focusing on the heritability of the left : right ratio of offspring, rather than on individual sidedness, is key for understanding how the direction of asymmetry becomes genetically assimilated.

Molecular phylogenetics reveals the evolutionary history of marine fishes (Actinopterygii) endemic to the subtropical islands of the Southwest Pacific.

Remote oceanic islands of the Pacific host elevated levels of actinopterygian (ray-finned fishes) endemism. Characterizing the evolutionary histories of these endemics has provided insight into the generation and maintenance of marine biodiversity in many regions. The subtropical islands of Lord Howe, Norfolk, and Rangitahua (Kermadec) in the Southwest Pacific are yet to be comprehensively studied. Here, we characterize the spatio-temporal diversification of marine fishes endemic to these Southwest Pacific islands by combining molecular phylogenies and the geographic distribution of species. We built Bayesian ultrametric trees based on open-access and newly generated sequences for five mitochondrial and ten nuclear loci, and using fossil data for time calibration. We present the most comprehensive phylogenies to date for marine ray-finned fish genera, comprising 34 species endemic to the islands, including the first phylogenetic placements for 11 endemics. Overall, our topologies confirm the species status of all endemics, including three undescribed taxa. Our phylogenies highlight the predominant affinity of these endemics with the Australian fish fauna (53%), followed by the East Pacific (15%), and individual cases where the closest sister taxon of our endemic is found in the Northwest Pacific and wider Indo-Pacific. Nonetheless, for a quarter of our focal endemics, their geographic affinity remains unresolved due to sampling gaps within their genera. Our divergence time estimates reveal that the majority of endemic lineages (67.6%) diverged after the emergence of Lord Howe (6.92 Ma), the oldest subtropical island in the Southwest Pacific, suggesting that these islands have promoted diversification. However, divergence ages of some endemics pre-date the emergence of the islands, suggesting they may have originated outside of these islands, or, in some cases, ages may be overestimated due to unsampled taxa. To fully understand the role of the Southwest Pacific subtropical islands as a 'cradle' for diversification, our study advocates for further regional surveys focused on tissue collection for DNA analysis.

Historical biogeography of the widespread macroalga Sargassum (Fucales, Phaeophyceae).

Sargassum is a cosmopolitan brown algal genus spanning the three ocean basins of the Atlantic, Pacific and Indian Oceans, inhabiting temperate, subtropical and tropical habitats. Sargassum has been postulated to have originated in the Oligocene epoch approximately 30 mya according to a broad phylogenetic analysis of brown macroalgae, but its diversification to become one of the most widespread and speciose macroalgal genera remains unclear. Here, we present a Bayesian molecular clock study, which analyzed data from the order Fucales of the brown algal crown radiation (BACR) group to reconstruct a time-calibrated phylogeny of the Sargassum clade. Our phylogeny included a total of 120 taxa with 99 Sargassum species sampled for three molecular markers - ITS-2, cox3 and rbcLS - calibrated with an unambiguous Sargassaceae fossil from between the lower and middle Miocene. The analysis revealed a much later origin of Sargassum than expected at about 6.7 mya, with the genus diversifying since approximately 4.3 mya. Current geographic distributions of Sargassum species were then analyzed in conjunction with the time-calibrated phylogeny using the dispersal-extinction-cladogenesis (DEC) model to estimate ancestral ranges of clades in the genus. Results strongly support origination of Sargassum in the Central Indo-Pacific (CIP) region with subsequent independent dispersal events into other marine realms. The longer history of diversification in the ancestral CIP range could explain the much greater diversity there relative to other marine areas today. Analyses of these dynamic processes, when fine-tuned to a higher spatial resolution, enable the identification of evolutionary hotspots and provide insights into long-term dispersal patterns.

Miocene climate change as a driving force for multiple origins of annual species in Astragalus (Fabaceae, Papilionoideae).

Astragalus, a highly diverse genus of flowering plants with its highest center of diversity in West Asia, is a classic example of rapid species-level radiation and adaptation to a diversity of habitats throughout the world. We examined the historical biogeography of Astragalus using molecular dating and ancestral area reconstruction to understand how past climate changes, geographical patterns and transition in life history have provoked diversification of Astragalus. Our results suggest that Astragalus probably originated during the middle Miocene in West Asia, underwent rapid diversification, subsequently and repeatedly expanded its range in the Mediterranean region, and later to North America through West Europe. This distribution range was also extended toward central and eastern Asia from the Middle Miocene to Pleistocene. Several climatic and geological processes during the Miocene-Pliocene may be implicated in the diversification of the major Astragalus clades. In particular, the annual lineages, which are important elements in the Mediterranean flora of Africa and Europe and in the deserts of southwest to central Asia, have arisen in response to progressing aridity from the late Miocene onwards (between 8.6 Ma and 2.98 Ma). Diversification rate analyses indicate three rapid and recent diversification events, one at c. 11 Ma in the clade that groups most of the Astragalus s.s. (all except the Ophiocarpus sister lineage), one at c. 5 Ma in the crown group of the Hypoglottis clade, including herbaceous annual and perennial species, and the most recent one at c. 3 Ma in the spiny cushion forming Astracantha clade. Our study highlights the complexity of processes and factors shaping diversifications in Astragalus; a complex interaction among climatic modifications providing opportunities for diversification and likely coincident with the evolution of key morphological and physiological adaptations.

A phylogeographic investigation of the kelp genus Laminaria (Laminariales, Phaeophyceae), with emphasis on the South Atlantic Ocean.

The genus Laminaria has a wide distribution range compared with other kelp genera because it is found in both the North and the South Atlantic, on both sides of the North Pacific, as well as in the Mediterranean. Hypotheses behind this biogeographical pattern have been discussed by several authors but have not yet been fully evaluated with time-calibrated phylogenies. Based on the analysis of four molecular markers (ITS2, rbcL, atp8 and trnWI), our goal was to reassess the Laminaria species diversity in South Africa, assess its relationship with the other species distributed in the South Atlantic and reconstruct the historical biogeography of the genus. Our results confirm the occurrence of a single species, L. pallida, in southern Africa, and its sister relationship with the North Atlantic L. ochroleuca. Both species belonged to a clade containing the other South Atlantic species: L. abyssalis from Brazil, and the Mediterranean L. rodriguezii. Our time-calibrated phylogenies suggest that Laminaria originated in the northern Pacific around 25 mya, followed by at least two migration events through the Bering Strait after its opening (~5.32 mya). Today, the first is represented by L. solidungula in the Arctic, while the second gave rise to the rest of the Atlantic species. The colonization of the North Atlantic was followed by a gradual colonization southward along the west coast of Europe, into the Mediterranean (~2.07 mya) and two recent, but disconnected, migrations (~1.34 and 0.87 mya) across the equator, giving rise to L. abyssalis in Brazil and L. pallida in southern Africa, respectively.

Complete mitochondrial genomes of living and extinct pigeons revise the timing of the columbiform radiation.

BACKGROUND: Pigeons and doves (Columbiformes) are one of the oldest and most diverse extant lineages of birds. However, the nature and timing of the group's evolutionary radiation remains poorly resolved, despite recent advances in DNA sequencing and assembly and the growing database of pigeon mitochondrial genomes. One challenge has been to generate comparative data from the large number of extinct pigeon lineages, some of which are morphologically unique and therefore difficult to place in a phylogenetic context. RESULTS: We used ancient DNA and next generation sequencing approaches to assemble complete mitochondrial genomes for eleven pigeons, including the extinct Ryukyu wood pigeon (Columba jouyi), the thick-billed ground dove (Alopecoenas salamonis), the spotted green pigeon (Caloenas maculata), the Rodrigues solitaire (Pezophaps solitaria), and the dodo (Raphus cucullatus). We used a Bayesian approach to infer the evolutionary relationships among 24 species of living and extinct pigeons and doves. CONCLUSIONS: Our analyses indicate that the earliest radiation of the Columbidae crown group most likely occurred during the Oligocene, with continued divergence of major clades into the Miocene, suggesting that diversification within the Columbidae occurred more recently than has been reported previously.

A multi-gene dataset reveals a tropical New World origin and Early Miocene diversification of croakers (Perciformes: Sciaenidae).

Widely distributed groups of living animals, such as the predominantly marine fish family Sciaenidae, have always attracted the attention of biogeographers to document the origins and patterns of diversification in time and space. In this study, the historical biogeography of the global Sciaenidae is reconstructed within a molecular phylogenetic framework to investigate their origin and to test the hypotheses explaining the present-day biogeographic patterns. Our data matrix comprises six mitochondrial and nuclear genes in 93 globally sampled sciaenid species from 52 genera. Within the inferred phylogenetic tree of the Sciaenidae, we identify 15 main and well-supported lineages; some of which have not been recognized previously. Reconstruction of habitat preferences shows repeated habitat transitions between marine and euryhaline environments. This implies that sciaenids can easily adapt to some variations in salinity, possibly as the consequence of their nearshore habitats and migratory life history. Conversely, complete marine/euryhaline to freshwater transitions occurred only three times, in South America, North America and South Asia. Ancestral range reconstruction analysis concomitant with fossil evidence indicates that sciaenids first originated and diversified in the tropical America during the Oligocene to Early Miocene before undergoing two range expansions, to Eastern Atlantic and to the Indo-West Pacific where a maximum species richness is observed. The uncommon biogeographic pattern identified is discussed in relation to current knowledge on origin of gradients of marine biodiversity toward the center of origin hypothesis in the Indo-West Pacific.

Bricklebush (Brickellia) phylogeny reveals dimensions of the great Asteraceae radiation in Mexico.

Data from molecular phylogenetics were used to assess aspects of diversity and relationships in Brickellia, a large and widespread genus of Eupatorieae. The dataset included sequence data from nuclear ribosomal ITS, ETS, and plastid psbA-trnH regions. An initial question was to assess the monophyly of the genus and whether Barroetea, Phanerostylis, and Kuhnia should be recognized as separate from or included in Brickellia. The results supported the hypothesis that Brickellia is monophyletic, with the small (2-3 species) Pleurocoronis as the sister group and showed Barroetea, Phanerostylis, and Kuhnia all embedded within the genus. Results of a time calibrated phylogeny from a BEAST analysis gave an estimated origination time for Brickellia at about 9 million years ago (Ma), with the oldest split within the genus dated at about 7.5Ma. A BAMM analysis based on the time calibrated tree showed that Brickellia has one rate shift in diversification associated with its origin in the late Miocene. Some lineages within the genus have had an increase in the rate of diversification over the past 5Ma, whereas other lineages have had a decrease in net diversification during this period. The results also elucidated nine clades within Brickellia which are accepted as taxonomic sections, and that will form logical units for future detailed studies.

Whole genome assembly and annotation of the endangered Caribbean coral Acropora cervicornis.

Coral species in the genus Acropora are key ecological components of coral reefs worldwide and represent the most diverse genus of scleractinian corals. While key species of Indo-Pacific Acropora have annotated genomes, no annotated genome has been published for either of the two species of Caribbean Acropora. Here we present the first fully annotated genome of the endangered Caribbean staghorn coral, Acropora cervicornis. We assembled and annotated this genome using high-fidelity nanopore long-read sequencing with gene annotations validated with mRNA sequencing. The assembled genome size is 318 Mb, with 28,059 validated genes. Comparative genomic analyses with other Acropora revealed unique features in A. cervicornis, including contractions in immune pathways and expansions in signaling pathways. Phylogenetic analysis confirms previous findings showing that A. cervicornis diverged from Indo-Pacific relatives around 41 million years ago, with the closure of the western Tethys Sea, prior to the primary radiation of Indo-Pacific Acropora. This new A. cervicornis genome enriches our understanding of the speciose Acropora and addresses evolutionary inquiries concerning speciation and hybridization in this diverse clade.

A second species of the pill millipede genus Nearctomeris Wesener, 2012 (Diplopoda, Glomerida) from the Great Smoky Mountains, USA.

We describe a second species of Nearctomeris Wesener, 2012, a genus of pill millipede endemic to the southern Appalachians, based on morphological and molecular evidence. The fauna of Glomerida in America is characterized by its low diversity, and Nearctomerissmokysp. nov. is only the fifth species of the order known from the eastern United States. Our phylogenetic analyses based on COI sequences recover a tentatively monophyletic lineage including both eastern American genera Onomeris Cook, 1896 and Nearctomeris, with a common ancestor in the Late Cretaceous to Mid Eocene and extant diversity within genera dating back to the Miocene. Our results suggest that the observed low diversity of the group in the eastern US is likely caused by extinction events, but it is also possible that new species are yet to be found. We provide new records for Nearctomerisinexpectata Wesener, 2012, Onomerisunderwoodi Cook, 1896 and O.australora Hoffman, 1950; the latter is here reported for the first time from South Carolina. We also present DNA barcoding data for all species of Glomerida present in the US that are not yet publicly available.

Interactions between breeding system and ploidy affect niche breadth in Solanum.

Understanding the factors driving ecological and evolutionary interactions of economically important plant species is important for agricultural sustainability. The geography of crop wild relatives, including wild potatoes (Solanum section Petota), have received attention; however, such information has not been analysed in combination with phylogenetic histories, genomic composition and reproductive systems to identify potential species for use in breeding for abiotic stress tolerance. We used a combination of ordinary least-squares (OLS) and phylogenetic generalized least-squares (PGLM) analyses to identify the discrete climate classes that make up the climate niche that wild potato species inhabit in the context of breeding system and ploidy. Self-incompatible diploid or self-compatible polyploid species significantly increase the number of discrete climate classes within a climate niche inhabited. This result was sustained when correcting for phylogenetic non-independence in the linear model. Our results support the idea that specific breeding system and ploidy combinations increase niche breadth through the decoupling of geographical range and niche diversity, and therefore, these species may be of particular interest for crop adaptation to a changing climate.

Characteristics of the complete mitochondrial genome of the monotypic genus Arctictis (Family: Viverridae) and its phylogenetic implications.

The binturong (Arctictis binturong) is classified as a member of the subfamily Paradoxurinae within the family Viverridae (Carnivora: Mammalia) and comprises nine subspecies spread across Southern and Southeast Asia. Here, we describe the complete mitochondrial genome of the Indian subspecies A. b. albifrons using next-generation sequencing methods. The total length of the A. b. albifrons mitogenome was 16,642 bp. Phylogenetic analyses based on 13 mitochondrial protein-coding genes placed the binturong as a sister taxon to Paguma larvata within the Paradoxurinae and supported the clustering of Genettinae and Viverrinae and the monophyly of Viverridae and six other families of feliforms, consistent with previous studies. Divergence time estimates suggest that the Viverridae diversified during the Miocene (22.62 Mya: 95% CI [20.78-24.54] Mya) and that Arctictis and Paguma split 12.57 Mya (95% CI [8.66-15.67] Mya). Further molecular studies are required to test the distinctiveness and diversity of the nine putative subspecies of binturong.