Evolutionary and Biogeographic Insights on the Macaronesian Beta-Patellifolia Species (Amaranthaceae) from a Time-Scaled Molecular Phylogeny

The Western Mediterranean Region and Macaronesian Islands are one of the top biodiversity hotspots of Europe, containing a significant native genetic diversity of global value among the Crop Wild Relatives (CWR). Sugar beet is the primary crop of the genus Beta (subfamily Betoideae, Amaranthaceae) and despite the great economic importance of this genus, and of the close relative Patellifolia species, a reconstruction of their evolutionary history is still lacking. We analyzed nrDNA (ITS) and cpDNA gene (matK, trnH-psbA, trnL intron, rbcL) sequences to: (i) investigate the phylogenetic relationships within the Betoideae subfamily, and (ii) elucidate the historical biogeography of wild beet species in the Western Mediterranean Region, including the Macaronesian Islands. The results support the Betoideae as a monophyletic group (excluding the Acroglochin genus) and provide a detailed inference of relationships within this subfamily, revealing: (i) a deep genetic differentiation between Beta and Patellifolia species, which may have occurred in Late Oligocene; and (ii) the occurrence of a West-East genetic divergence within Beta, indicating that the Mediterranean species probably differentiated by the end of the Miocene. This was interpreted as a signature of species radiation induced by dramatic habitat changes during the Messinian Salinity Crisis (MSC, 5.96–5.33 Mya). Moreover, colonization events during the Pleistocene also played a role in shaping the current diversity patterns among and within the Macaronesian Islands. The origin and number of these events could not be revealed due to insufficient phylogenetic resolution, suggesting that the diversification was quite recent in these archipelagos, and unravelling potential complex biogeographic patterns with hybridization and gene flow playing an important role. Finally, three evolutionary lineages were identified corresponding to major gene pools of sugar beet wild relatives, which provide useful information for establishing in situ and ex situ conservation priorities in the hotspot area of the Macaronesian Islands.     

Colonization and diversification of the spider genus Pholcus Walckenaer, 1805 (Araneae, Pholcidae) in the Macaronesian archipelagos: evidence for long-term occupancy yet rapid recent speciation

Macaronesian archipelagos stand apart from other oceanic islands reputed as laboratories for the study of evolution by their proximity to the mainland, lack of subsidence, and steep ecological gradients. The genus Pholcus Walckenaer, 1805, commonly known as daddy-long-leg spiders, is one of the most speciose arthropod groups in the region, with 25 endemic species. In the present study, we use information from four mitochondrial genes, along with morphological data, to examine the phylogenetic relationships and diversification patterns of the genus in the region. Phylogenetic analyses support monophyly of Macaronesian Pholcus including the Moroccan species Pholcus vachoni and hence a single colonization event in the archipelagos. Madeira colonizers most likely originated from the Canaries, and a back-colonization of the nearby mainland receives further support. Estimated lineage divergence times suggest a long-time presence of Pholcus in the region, but also reveal that most present-day species are the result of recent, and probably rapid, speciation events. Diagnostic characters among Macaronesian Pholcus are confined to structures involved in copulation. Coupled with the extremely high diversification rate, the highest recorded for spiders, these copulatory characters suggest that sexual selection has played a key role in the local diversification of Pholcus in Macaronesia.     

Macaronesia: a source of hidden genetic diversity for post‐glacial recolonization of western Europe in the leafy liverwort Radula lindenbergiana

Aim Bryophytes exhibit apparently low rates of endemism in Macaronesia and differ from angiosperms in their diversity patterns by the widespread occurrence of endemics within and among archipelagos. This paper investigates the phylogeography of the leafy liverwort Radula lindenbergiana to determine: (1) whether or not morphologically cryptic diversification has occurred in Macaronesia, and (2) the relationships between Macaronesian and continental populations. Location Macaronesia, Europe, Africa. Methods Eighty‐four samples were collected across the species’ distribution range and sequenced at four chloroplast DNA (cpDNA) loci (atpB–rbcL, trnG, trnL and rps4). Phylogenetic reconstructions and Bayesian ancestral area reconstructions were used in combination with population genetics statistics (H, N_ST, F_ST) to describe the pattern of present genetic diversity in R. lindenbergiana and infer its biogeographic history. Results Patterns of genetic diversity in R. lindenbergiana exhibit a striking westwards gradient, wherein haplotype (0.90) and nucleotide (0.0038 ± 0.0019) diversity peak in Macaronesia, with a substantial endemic component. We found 20.9% of the genetic variance between biogeographic regions, and most pairwise F_ST comparisons between regions are significantly different from zero. The global N_ST (0.78) is significantly higher than the global F_ST (0.20), providing evidence for the presence of phylogeographic signal in the data. Ancestral area reconstructions suggest that the haplotypes currently found in western Europe share a Macaronesian common ancestor. Main conclusions The haplotype diversification exhibited by R. lindenbergiana in Macaronesia is comparable to that reported for many angiosperm groups at the species level. The apparent lack of radiation among Macaronesian bryophytes may thus reflect the reduced morphology of bryophytes in comparison with angiosperms. The high diversity found among Macaronesian haplotypes, especially in Madeira and the Canary Islands, and the significant N_ST/F_ST ratio between Macaronesia and all the other biogeographic regions (an indication that mutation rate exceeds dispersal rates) suggest that Macaronesian archipelagos could have served as a refugium during the Quaternary glaciations. Many haplotypes currently found in Europe share a Macaronesian common ancestor, and this further suggests that Macaronesia might have played a key role in the back‐colonization of the continent.     

Molecular phylogeny ofCheirolophus (Asteraceae:Cardueae-Centaureinae) based on ITS sequences of nuclear ribosomal DNA

The genusCheirolophus has an interesting western Mediterranean and Macaronesian distribution. Here we investigate the delimitation of the genus and its exclusion from the large genusCentaurea, the systematic position of the related genusPaleocyanus, the delimitation of some species and the phylogeny of the group. We have carried out a phylogenetic analysis of the PCR-generated sequences of the internal transcribed spacers (ITS-1 and ITS-2) of the nuclear ribosomal DNA. The results suggest that the genus, includingPaleocyanus crassifolius is monophyletic; thus, a new combination of this species underCheirolophus is proposed. The Macaronesian group of species is also monophyletic, indicating a single colonization of the archipelago. The poor resolution of microspecies in the Macaronesian group reinforces the hypothesis of a very recent differentiation of the group.     

Reconstruction of the spatio-temporal diversification and ecological niche evolution of Helianthemum (Cistaceae) in the Canary Islands using genotyping-by-sequencing data

Background and AimsSeveral biogeographical models have been proposed to explain the colonization and diversification patterns of Macaronesian lineages. In this study, we calculated the diversification rates and explored what model best explains the current distribution of the 15 species endemic to the Canary Islands belonging to Helianthemum sect. Helianthemum (Cistaceae).MethodsWe performed robust phylogenetic reconstructions based on genotyping-by-sequencing data and analysed the timing, biogeographical history and ecological niche conservatism of this endemic Canarian clade.Key ResultsOur phylogenetic analyses provided strong support for the monophyly of this clade, and retrieved five lineages not currently restricted to a single island. The pristine colonization event took place in the Pleistocene (~1.82 Ma) via dispersal to Tenerife by a Mediterranean ancestor.ConclusionsThe rapid and abundant diversification (0.75–1.85 species per million years) undergone by this Canarian clade seems the result of complex inter-island dispersal events followed by allopatric speciation driven mostly by niche conservatism, i.e. inter-island dispersal towards niches featuring similar environmental conditions. Nevertheless, significant instances of ecological niche shifts have also been observed in some lineages, making an important contribution to the overall diversification history of this clade.     

Recent origin,active speciation and dispersal for the lichen genus Nephroma (Peltigerales) in Macaronesia

Aim We reconstructed the phylogeny of the lichen genus Nephroma (Peltigerales) to assess the relationships of species endemic to Macaronesia. We estimated dates of divergences to test the hypothesis that the species arose in Macaronesia (neo‐endemism) versus the oceanic archipelagos serving as refugia for formerly widespread taxa (palaeo‐endemism). Location Cosmopolitan with a special focus on the archipelagos of the Azores, Madeira and the Canary Islands. Methods DNA sequences were obtained from 18 species for three loci and analysed using maximum parsimony, maximum likelihood and Bayesian inferences. Divergence dates were estimated for the internal transcribed spacer (ITS)‐based phylogeny using a relaxed molecular clock. Reconstruction of the ancestral geographical range was conducted using the Bayesian 50% majority rule consensus tree under a parsimony method. Results The backbone phylogenetic tree was fully supported, with Nephroma plumbeum as sister to all other species. Four strongly supported clades were detected: the Nephroma helveticum, the N. bellum, the N. laevigatum and the N. parile clades. The latter two share a common ancestor and each includes a widespread Holarctic species (N. laevigatum and N. parile, respectively) and all species endemic to Macaronesia. The data suggest a neo‐endemic origin of Macaronesian taxa, a recent range expansion from Macaronesia of both widespread species, a range expansion limited to the Mediteranean Basin and south‐western Europe for another taxon, and a long dispersal event that resulted in a speciation event in the western parts of North America. Main conclusions The Macaronesian endemic species belong to two sister clades and originated from a most recent common ancestor (MRCA) shared with one widely distributed taxon, either N. parile or N. laevigatum. Estimates of the mean divergence dates suggest that the endemics originated in the archipelagos after the rise of the volcanic islands, along with the ancestor to the now widespread species, which probably expanded their range beyond Macaronesia via long‐distance dispersal. This study provides the first phylogenetic evidence of Macaronesian neo‐endemism in lichenized fungi and provides support for the hypothesis that oceanic islands may serve as a source for the colonization of continents. However, further data are needed to properly assess the alternative hypothesis, namely colonization from western North America.     

Evolution,systematics and historical biogeography of sand flies of the subgenus Paraphlebotomus (Diptera,Psychodidae, Phlebotomus) inferred using restriction-site associated DNA markers

Phlebotomine sand flies are the main natural vectors of Leishmania, which cause visceral and tegumentary tropical diseases worldwide. However, their taxonomy and evolutionary history remain poorly studied. Indeed, as for many human disease vectors, their small size is a challenge for morphological and molecular works. Here, we successfully amplified unbiased copies of whole genome to sequence thousands of restriction-site associated DNA (RAD) markers from single specimens of phlebotomines. RAD markers were used to infer a fully resolved phylogeny of the subgenus Paraphlebotomus (11 species + 5 outgroups, 32 specimens). The subgenus was not recovered as monophyletic and we describe a new subgenus Artemievus subg. nov. Depaquit for Phlebotomus alexandri. We also confirm the validity of Ph. riouxi which is reinstated as valid species. Our analyses suggest that Paraphlebotomus sensu nov. originated ca 12.9–8.5 Ma and was possibly largely distributed from peri-Mediterranean to Irano-Turanian regions. Its biogeographical history can be summarized into three phases: i) a first split between Ph. riouxi + Ph. chabaudi and other species that may have resulted from the rise of the Saharan belt ca 8.5 Ma; ii) a Messinian vicariant event (7.3–5.3 Ma) during which the prolonged drought could have resulted in the divergence of main lineages; iii) a recent radiation event (3–2 Ma) that correspond to cycles of wet and dry periods in the Middle East and the East African subregions during the Pleistocene. Interestingly these cycles are also hypothetical drivers of the diversification of rodents, in the burrows of which Paraphlebotomus larvae develop. By meeting the challenge of sequencing pangenomics markers from single, minute phlebotomines, this work opens new avenues for improving our understanding of the epidemiology of leishmaniases and possibly other human diseases transmitted by arthropod vectors.     

Phylogeography and molecular phylogeny of Macaronesian island Tarphius (Coleoptera: Zopheridae): why are there so few species in the Azores?

Aim We used a phylogenetic framework to examine island colonization and predictions pertaining to differentiation within Macaronesian Tarphius (Insecta, Coleoptera, Zopheridae), and explain the paucity of endemics in the Azores compared with other Macaronesian archipelagos. Specifically, we test whether low diversity in the Azores could be due to recent colonization (phylogenetic lineage youth), cryptic speciation (distinct phylogenetic entities within species) or the young geological age of the archipelago. Location Macaronesian archipelagos (Azores, Madeira and the Canary Islands), northern Portugal and Morocco. Methods Phylogenetic analyses of mitochondrial and nuclear genes of Tarphius beetles of the Azores, other Macaronesian islands and neighbouring continental areas were used to investigate the origin of island biodiversity and to compare patterns of colonization and differentiation. A comparative nucleotide substitution rate test was used to select the appropriate substitution rate to infer clade divergence times. Results Madeiran and Canarian Tarphius species were found to be more closely related to each other, while Azorean taxa grouped separately. Azorean taxa showed concordance between species and phylogenetic clades, except for species that occur on multiple islands, which segregated by island of origin. Divergence time estimates revealed that Azorean Tarphius are an old group and that the most recent intra‐island speciation event on Santa Maria, the oldest island, occurred between 3.7 and 6.1 Ma. Main conclusions Our phylogenetic approach provides new evidence to understand the impoverishment of Azorean endemics: (1) Tarphius have had a long evolutionary history within the Azores, which does not support the hypothesis of fewer radiation events due to recent colonization; (2) the current taxonomy of Azorean Tarphius does not reflect common ancestry and cryptic speciation is responsible for the underestimation of endemics; (3) intra‐island differentiation in the Azores was found only in the oldest island, supporting the idea that young geological age of the archipelago limits the number of endemics; and (4) the lack of evidence for recent intra‐island diversification in Santa Maria could also explain the paucity of Azorean endemics. Phylogenetic reconstructions of other species‐rich taxa that occur on multiple Macaronesian archipelagos will reveal whether our conclusions are taxon specific, or of a more general nature.     

Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds and reptiles

Rates of biological diversification should ultimately correspond to rates of genome evolution. Recent studies have compared diversification rates with phylogenetic branch lengths, but incomplete phylogenies hamper such analyses for many taxa. Herein, we use pairwise comparisons of confamilial sauropsid (bird and reptile) mitochondrial DNA (mtDNA) genome sequences to estimate substitution rates. These molecular evolutionary rates are considered in light of the age and species richness of each taxonomic family, using a random-walk speciation–extinction process to estimate rates of diversification. We find the molecular clock ticks at disparate rates in different families and at different genes. For example, evolutionary rates are relatively fast in snakes and lizards, intermediate in crocodilians and slow in turtles and birds. There was also rate variation across genes, where non-synonymous substitution rates were fastest at ATP8 and slowest at CO3. Family-by-gene interactions were significant, indicating that local clocks vary substantially among sauropsids. Most importantly, we find evidence that mitochondrial genome evolutionary rates are positively correlated with speciation rates and with contemporary species richness. Nuclear sequences are poorly represented among reptiles, but the correlation between rates of molecular evolution and species diversification also extends to 18 avian nuclear genes we tested. Thus, the nuclear data buttress our mtDNA findings.     

Genetic markers in Andean Puya species (Bromeliaceae) with implications on plastome evolution and phylogeny

The Andean plant endemic Puya is a striking example of recent and rapid diversification from central Chile to the northern Andes, tracking mountain uplift. This study generated 12 complete plastomes representing nine Puya species and compared them to five published plastomes for their features, genomic evolution, and phylogeny. The total size of the Puya plastomes ranged from 159,542 to 159,839 bp with 37.3%–37.4% GC content. The Puya plastomes were highly conserved in organization and structure with a typical quadripartite genome structure. Each of the 17 consensus plastomes harbored 133 genes, including 87 protein‐coding genes, 38 tRNA (transfer RNA) genes, and eight rRNA (ribosomal RNA) genes; we found 69–78 tandem repeats, 45–60 SSRs (simple sequence repeats), and 8–22 repeat structures among 13 species. Four protein‐coding genes were identified under positive site‐specific selection in Puya. The complete plastomes and hypervariable regions collectively provided pronounced species discrimination in Puya and a practical tool for future phylogenetic studies. The reconstructed phylogeny and estimated divergence time for the lineage suggest that the diversification of Puya is related to Andean orogeny and Pleistocene climatic oscillations. This study provides plastome resources for species delimitation and novel phylogenetic and biogeographic studies.     

Old Lineages in a New Ecosystem: Diversification of Arcellinid Amoebae (Amoebozoa) and Peatland Mosses

Arcellinid testate amoebae (Amoebozoa) form a group of free-living microbial eukaryotes with one of the oldest fossil records known, yet several aspects of their evolutionary history remain poorly understood. Arcellinids occur in a range of terrestrial, freshwater and even brackish habitats; however, many arcellinid morphospecies such as Hyalosphenia papilio are particularly abundant in Sphagnum-dominated peatlands, a relatively new ecosystem that appeared during the diversification of Sphagnum species in the Miocene (5–20 Myr ago). Here, we reconstruct divergence times in arcellinid testate amoebae after selecting several fossils for clock calibrations and then infer whether or not arcellinids followed a pattern of diversification that parallels the pattern described for Sphagnum. We found that the diversification of core arcellinids occurred during the Phanerozoic, which is congruent with most arcellinid fossils but not with the oldest known amoebozoan fossil (i.e. at ca. 662 or ca. 750 Myr). Overall, Sphagnum and the Hyalospheniidae exhibit different patterns of diversification. However, an extensive molecular phylogenetic analysis of distinct clades within H. papilio species complex demonstrated a correlation between the recent diversification of H. papilio, the recent diversification of Sphagnum mosses, and the establishment of peatlands.     

Evolution of Asian Interior Arid-Zone Biota: Evidence from the Diversification of Asian Zygophyllum (Zygophyllaceae)

The Asian interior arid zone is the largest desert landform system in the Northern Hemisphere, and has high biodiversity. Little is currently known about the evolutionary history of its biota. In this study, we used Zygophyllum, an important and characteristic component of the Asian interior arid zone, to provide new insights into the evolution of this biota. By greatly enlarged taxon sampling, we present the phylogenetic analysis of Asian Zygophyllum based on two plastid and one nuclear markers. Our phylogenetic analyses indicate that Asian Zygophyllum and Sarcozygium form a clade and Sarcozygium is further embedded within the shrub subclade. An integration of phylogenetic, biogeographic, and molecular dating methods indicates that Zygophyllum successfully colonized the Asian interior from Africa in the early Oligocene, and Asian Zygophyllum became differentiated in the early Miocene and underwent a burst of diversification in the late Miocene associated with the expansion of Asian interior arid lands due to orogenetic and climatic changes. Combining diversification patterns of other important components of the Asian interior arid zone, we propose a multi-stage evolution model for this biota: the late Eocene–early Oligocene origin, the early Miocene expansion, and the middle-late Miocene rapid expansion to the whole Asian interior arid zone. This study also demonstrates that, for Zygophyllum and perhaps other arid-adapted organisms, arid biomes are evolutionary cradles of diversity.     

Eutherians experienced elevated evolutionary rates in the immediate aftermath of the Cretaceous–Palaeogene mass extinction

The effect of the Cretaceous–Palaeogene (K–Pg) mass extinction on the evolution of many groups, including placental mammals, has been hotly debated. The fossil record suggests a sudden adaptive radiation of placentals immediately after the event, but several recent quantitative analyses have reconstructed no significant increase in either clade origination rates or rates of character evolution in the Palaeocene. Here we use stochastic methods to date a recent phylogenetic analysis of Cretaceous and Palaeocene mammals and show that Placentalia likely originated in the Late Cretaceous, but that most intraordinal diversification occurred during the earliest Palaeocene. This analysis reconstructs fewer than 10 placental mammal lineages crossing the K–Pg boundary. Moreover, we show that rates of morphological evolution in the 5 Myr interval immediately after the K–Pg mass extinction are three times higher than background rates during the Cretaceous. These results suggest that the K–Pg mass extinction had a marked impact on placental mammal diversification, supporting the view that an evolutionary radiation occurred as placental lineages invaded new ecological niches during the Early Palaeocene.     

Rapid diversification associated with ecological specialization in Neotropical Adelpha butterflies

Rapid diversification is often associated with morphological or ecological adaptations that allow organisms to radiate into novel niches. Neotropical Adelpha butterflies, which comprise over 200 species and subspecies, are characterized by extraordinary breadth in host plant use and wing colour patterns compared to their closest relatives. To examine the relationship between phenotypic and species diversification, we reconstructed the phylogenetic history of Adelpha and its temperate sister genus Limenitis using genomewide restriction‐site‐associated DNA (RAD) sequencing. Despite a declining fraction of shared markers with increasing evolutionary distance, the RAD‐Seq data consistently generated well‐supported trees using a variety of phylogenetic methods. These well‐resolved phylogenies allow the identification of an ecologically important relationship with a toxic host plant family, as well as the confirmation of widespread, convergent wing pattern mimicry throughout the genus. Taken together, our results support the hypothesis that evolutionary innovations in both larvae and adults have permitted the colonization of novel host plants and fuelled adaptive diversification within this large butterfly radiation.     

Molecular evidence that the genes for dioecism and monoecism in Spinacia oleracea L. are located at different loci in a chromosomal region

Spinach (Spinacia oleracea L.) is widely known to be dioecious. However, monoecious plants can also occur in this species. Sex expression in dioecious spinach plants is controlled by a single gene pair termed X and Y. Our previous study showed that a single, incompletely dominant gene, which controls the monoecious condition in spinach line 03–336, should be allelic or linked to X/Y. Here, we developed 19 AFLP markers closely linked to the monoecious gene. The AFLP markers were mapped to a 38.2-cM chromosomal region that included the monoecious gene, which is bracketed between flanking markers with a distance of 7.1 cM. The four AFLP markers developed in our studies were converted into sequence-characterized amplified region (SCAR) markers, which are linked to both the monoecious gene and Y and are common to both populations segregating for the genes. Linkage analysis using the SCAR markers suggested that the monoecious gene (M) and Y are located in different intervals, between different marker pairs. Analysis of populations segregating for both M and Y also directly demonstrates linkage of the genes at a distance of ∼12 cM. The data presented in this study may be useful for breeding dioecious and highly male monoecious lines utilized as the pollen parents for hybrid seed production, as well as for studies of the evolutionary history of sexual systems in this species, and can provide a molecular basis for positional cloning of the sex-determining genes.     

Relationships of the Macaronesian and Mediterranean floras: molecular evidence for multiple colonizations into Macaronesia and back-colonization of the continent in Convolvulus (Convolvulaceae)

A molecular phylogenetic analysis of the Macaronesian endemic species of Convolvulus was undertaken using data from the nuclear ribosomal internal transcribed spacer (ITS) regions. The results of the analysis support two introductions into Macaronesia from distantly related clades within Convolvulus and a subsequent back-colonization to the continent from within one of the clades. Hypothesized relationships between Macaronesian species and New World taxa and between the Canarian endemic C. caput-medusae and the Moroccan C. trabutianus are refuted. Both Macaronesian clades are shown to have Mediterranean sister groups although one is predominantly western Mediterranean and the other predominantly eastern Mediterranean in distribution. The patterns of colonization into Macaronesia demonstrated by Convolvulus and also by other multiple colonizing genera conform to either a pattern of phylogenetic distinctiveness or a checkerboard distribution of island lineages. Both are consistent with the hypothesis that niche preemption is responsible for the limited number of colonizations into the region. A review of sister group relationships demonstrates that, in common with Convolvulus, most Macaronesian groups have sister groups distributed in the near-continent (i.e., western Mediterranean). Disjunct sister group relationships (including Eastern Mediterranean disjunctions) occur in only 18% of groups.     

Birds are islands for parasites

Understanding the mechanisms driving the extraordinary diversification of parasites is a major challenge in evolutionary biology. Co-speciation, one proposed mechanism that could contribute to this diversity is hypothesized to result from allopatric co-divergence of host–parasite populations. We found that island populations of the Galápagos hawk (Buteo galapagoensis) and a parasitic feather louse species (Degeeriella regalis) exhibit patterns of co-divergence across variable temporal and spatial scales. Hawks and lice showed nearly identical population genetic structure across the Galápagos Islands. Hawk population genetic structure is explained by isolation by distance among islands. Louse population structure is best explained by hawk population structure, rather than isolation by distance per se, suggesting that lice tightly track the recent population histories of their hosts. Among hawk individuals, louse populations were also highly structured, suggesting that hosts serve as islands for parasites from an evolutionary perspective. Altogether, we found that host and parasite populations may have responded in the same manner to geographical isolation across spatial scales. Allopatric co-divergence is likely one important mechanism driving the diversification of parasites.     

AN ADAPTIVE RADIATION OF FROGS IN A SOUTHEAST ASIAN ISLAND ARCHIPELAGO

Living amphibians exhibit a diversity of ecologies, life histories, and species‐rich lineages that offers opportunities for studies of adaptive radiation. We characterize a diverse clade of frogs (Kaloula, Microhylidae) in the Philippine island archipelago as an example of an adaptive radiation into three primary habitat specialists or ecotypes. We use a novel phylogenetic estimate for this clade to evaluate the tempo of lineage accumulation and morphological diversification. Because species‐level phylogenetic estimates for Philippine Kaloula are lacking, we employ dense population sampling to determine the appropriate evolutionary lineages for diversification analyses. We explicitly take phylogenetic uncertainty into account when calculating diversification and disparification statistics and fitting models of diversification. Following dispersal to the Philippines from Southeast Asia, Kaloula radiated rapidly into several well‐supported clades. Morphological variation within Kaloula is partly explained by ecotype and accumulated at high levels during this radiation, including within ecotypes. We pinpoint an axis of morphospace related directly to climbing and digging behaviors and find patterns of phenotypic evolution suggestive of ecological opportunity with partitioning into distinct habitat specialists. We conclude by discussing the components of phenotypic diversity that are likely important in amphibian adaptive radiations.     

Evolutionary Genomics and Adaptive Evolution of the Hedgehog Gene Family (Shh,Ihh and Dhh) in Vertebrates

The Hedgehog (Hh) gene family codes for a class of secreted proteins composed of two active domains that act as signalling molecules during embryo development, namely for the development of the nervous and skeletal systems and the formation of the testis cord. While only one Hh gene is found typically in invertebrate genomes, most vertebrates species have three (Sonic hedgehog – Shh; Indian hedgehog – Ihh; and Desert hedgehog – Dhh), each with different expression patterns and functions, which likely helped promote the increasing complexity of vertebrates and their successful diversification. In this study, we used comparative genomic and adaptive evolutionary analyses to characterize the evolution of the Hh genes in vertebrates following the two major whole genome duplication (WGD) events. To overcome the lack of Hh-coding sequences on avian publicly available databases, we used an extensive dataset of 45 avian and three non-avian reptilian genomes to show that birds have all three Hh paralogs. We find suggestions that following the WGD events, vertebrate Hh paralogous genes evolved independently within similar linkage groups and under different evolutionary rates, especially within the catalytic domain. The structural regions around the ion-binding site were identified to be under positive selection in the signaling domain. These findings contrast with those observed in invertebrates, where different lineages that experienced gene duplication retained similar selective constraints in the Hh orthologs. Our results provide new insights on the evolutionary history of the Hh gene family, the functional roles of these paralogs in vertebrate species, and on the location of mutational hotspots.