Burst Of Diversification Research Articles

Bursts of Rapid Diversification, Dispersals Out of Southern Africa, and Two Origins of Dioecy Punctuate the Evolution of Asparagus.

The genus Asparagus arose ∼9 to 15 million years ago (Ma), and transitions from hermaphroditism to dioecy (separate sexes) occurred ∼3 to 4 Ma. Roughly 27% of extant Asparagus species are dioecious, while the remaining are bisexual with monoclinous flowers. As such, Asparagus is an ideal model taxon for studying the early stages of dioecy and sex chromosome evolution in plants. Until now, however, understanding of diversification and shifts from hermaphroditism to dioecy in Asparagus has been hampered by the lack of robust species tree estimates for the genus. In this study, a genus-wide phylogenomic analysis including 1,726 nuclear loci and comprehensive species sampling supports two independent origins of dioecy in Asparagus-first in a widely distributed Eurasian clade and then in a clade restricted to the Mediterranean Basin. Modeling of ancestral biogeography indicates that both dioecy origins were associated with range expansion out of southern Africa. Our findings also reveal several bursts of diversification across the phylogeny, including an initial radiation in southern Africa that gave rise to 12 major clades in the genus, and more recent radiations that have resulted in paraphyly and polyphyly among closely related species, as expected given active speciation processes. Lastly, we report that the geographic origin of domesticated garden asparagus (Asparagus officinalis L.) was likely in western Asia near the Mediterranean Sea. The presented phylogenomic framework for Asparagus is foundational for ongoing genomic investigations of diversification and functional trait evolution in the genus and contributes to its utility for understanding the origin and early evolution of dioecy and sex chromosomes.

Genomic patterns in the dwarf kingfishers of northern Melanesia reveal a mechanistic framework explaining the paradox of the great speciators

Abstract The paradox of the great speciators describes a contradictory biogeographic pattern exhibited by numerous avian lineages in Oceania. Specifically, these lineages display broad geographic distributions across the region, implying strong over-water dispersal capabilities; yet, they also display repeated genetic and phenotypic divergence—even between geographically proximate islands—implying poor inter-island dispersal capabilities. One group originally cited as evidence for this paradox is the dwarf kingfishers of the genus Ceyx. Here, using genomic sequencing and comprehensive geographic sampling of the monophyletic Ceyx radiation from northern Melanesia, we find repeated, deep genetic divergence and no evidence for gene flow between lineages found on geographically proximate islands, providing an exceptionally clear example of the paradox of the great speciators. A dated phylogenetic reconstruction suggests a significant burst of diversification occurred rapidly after reaching northern Melanesia, between 3.9 and 2.9 MYA. This pattern supports a shift in net diversification rate, concordant with the expectations of the “colonization cycle” hypothesis, which implies a historical shift in dispersiveness among great speciator lineages during the evolutionary past. Here, we present a formalized framework that explains how repeated founder effects and shifting selection pressures on highly dispersive genotypes are the only ultimate causes needed to generate the paradox of the great speciators. Within this framework, we emphasize that lineage-specific traits and island-specific abiotic factors will result in varying levels of selection pressure against dispersiveness, caused by varying proximate eco-evolutionary mechanisms. Overall, we highlight how understanding patterns of diversification in the Ceyx dwarf kingfishers helped us generate a cohesive framework that provides a rigorous mechanistic explanation for patterns concordant with the paradox of the great speciators and the repeated emergence of geographic radiations in island archipelagoes across the globe.

Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification.

Bryophytes form a major component of terrestrial plant biomass, structuring ecological communities in all biomes. Our understanding of the evolutionary history of hornworts, liverworts, and mosses has been significantly reshaped by inferences from molecular data, which have highlighted extensive homoplasy in various traits and repeated bursts of diversification. However, the timing of key events in the phylogeny, patterns, and processes of diversification across bryophytes remain unclear. Using the GoFlag probe set, we sequenced 405 exons representing 228 nuclear genes for 531 species from 52 of the 54 orders of bryophytes. We inferred the species phylogeny from gene tree analyses using concatenated and coalescence approaches, assessed gene conflict, and estimated the timing of divergences based on 29 fossil calibrations. The phylogeny resolves many relationships across the bryophytes, enabling us to resurrect five liverwort orders and recognize three more and propose 10 new orders of mosses. Most orders originated in the Jurassic and diversified in the Cretaceous or later. The phylogenomic data also highlight topological conflict in parts of the tree, suggesting complex processes of diversification that cannot be adequately captured in a single gene-tree topology. We sampled hundreds of loci across a broad phylogenetic spectrum spanning at least 450 Ma of evolution; these data resolved many of the critical nodes of the diversification of bryophytes. The data also highlight the need to explore the mechanisms underlying the phylogenetic ambiguity at specific nodes. The phylogenomic data provide an expandable framework toward reconstructing a comprehensive phylogeny of this important group of plants.

Social Plasticity Enhances Signal-Preference Codivergence.

AbstractThe social environment is often the most dynamic and fitness-relevant environment animals experience. Here we tested whether plasticity arising from variation in social environments can promote signal-preference divergence-a key prediction of recent speciation theory but one that has proven difficult to test in natural systems. Interactions in mixed social aggregations could reduce, create, or enhance signal-preference differences. In the latter case, social plasticity could establish or increase assortative mating. We tested this by rearing two recently diverged species of Enchenopa treehoppers-sap-feeding insects that communicate with plant-borne vibrational signals-in treatments consisting of mixed-species versus own-species aggregations. Social experience with heterospecifics (in the mixed-species treatment) resulted in enhanced signal-preference species differences. For one of the two species, we tested but found no differences in the plastic response between sympatric and allopatric sites, suggesting the absence of reinforcement in the signals and preferences and their plastic response. Our results support the hypothesis that social plasticity can create or enhance signal-preference differences and that this might occur in the absence of long-term selection against hybridization on plastic responses themselves. Such social plasticity may facilitate rapid bursts of diversification.

The synergy of abiotic and biotic factors correlated with diversification of Fumarioideae (Papaveraceae) in the Cenozoic

Rapid diversification of a group is often associated with exploiting an ecological opportunity and/or the evolution of a key innovation. However, how the interplay of such abiotic and biotic factors correlates with organismal diversification has been rarely documented in empirical studies, especially for organisms inhabiting drylands. Fumarioideae is the largest subfamily in Papaveraceae and is mainly distributed in temperate regions of the Northern Hemisphere. Here, we used one nuclear (ITS) and six plastid (rbcL, atpB, matK, rps16, trnL-F, and trnG) DNA sequences to investigate the spatio-temporal patterns of diversification and potential related factors of this subfamily. We first present the most comprehensive phylogenetic analysis of Fumarioideae to date. The results of our integrated molecular dating and biogeographic analyses indicate that the most recent common ancestor of Fumarioideae started to diversify in Asia during the Upper Cretaceous, and then dispersed multiple times out of Asia in the Cenozoic. In particular, we discover two independent dispersal events from Eurasia to East Africa in the late Miocene, suggesting that the Arabian Peninsula might be an important exchange corridor between Eurasia and East Africa in the late Miocene. Within the Fumarioideae, increased speciation rates were detected in two groups, Corydalis and Fumariinae. Corydalis first experienced a burst of diversification in its crown group at ∼ 42 Ma, and further accelerated diversification from the mid-Miocene onwards. During these two periods, Corydalis had evolved diverse life history types, which could have facilitated the colonization of diverse habitats originating from extensive orogenesis in the Northern Hemisphere as well as Asian interior desertification. Fumariinae underwent a burst of diversification at ∼ 15 Ma, which temporally coincides with the increasing aridification in central Eurasia, but is markedly posterior to the shifts in habitat (from moist to arid) and in life history (from perennial to annual) and to range expansion from Asia to Europe, suggesting that Fumariinae species may have been pre-adapted to invade European arid habitats by the acquisition of annual life history. Our study provides an empirical case that documents the importance of pre-adaptation on organismal diversification in drylands and highlights the significant roles of the synergy of abiotic and biotic factors in promoting plant diversification.

Diversification of cephalic shield shape and antenna in phyllosoma I of slipper and spiny lobsters (Decapoda: Achelata)

Slipper (Scyllaridae) and spiny (Palinuridae) lobsters show a complex life cycle with a planktonic larval phase, named phyllosoma. This unique larval form within Achelata (Decapoda) is characterized by a transparent dorsoventrally compressed body and a pair of antennae. This conspicuous morphology has been attributed to adaptive specialization of planktonic life. Early studies suggest that phyllosoma morphology has remained constant over the evolutionary history of Achelata, while recent evidence points out large morphological changes and that diversification of phyllosoma larvae is a consequence of radiation and specialization processes to exploit different habitats. Given the ecological and evolutive significance of phyllosoma, we used shape variation of the first phyllosoma stage (phyllosoma I) and a time-calibrated phylogeny of extant Achelata to study how diversification of phyllosoma I shape occurred along with the evolutionary history of Achelata. Our results show a conserved phyllosoma I with a pear-shaped cephalic shield and large antennae in spiny lobsters and older groups of slipper lobsters, yet highly specialized phyllosoma I with wide rounded cephalic shield and short antennae in younger groups of slipper lobsters. Analyses revealed two bursts of lineage diversification in mid and late history without a slowdown in recent times. Both bursts preceded large bursts of morphological disparity. These results joined with the allopatric distribution of species and convergence of phyllosoma I shapes between largely divergent groups suggest that diversification involves nonadaptive radiation processes. However, the correlation of a major direction of shape with the maximum distribution depth of adults and the occurrence of the second burst of diversification post-extinction of competitors within Achelata presuppose some ecological opportunities that might have promoted lineage and morphological diversification, fitting to the characteristic components of adaptive radiations. Therefore, we conclude that diversification of Achelata presents a main signature of nonadaptive radiation with some components of adaptive radiation.

Combining palaeontological and neontological data shows a delayed diversification burst of carcharhiniform sharks likely mediated by environmental change

Estimating deep-time species-level diversification processes remains challenging. Both the fossil record and molecular phylogenies allow the estimation of speciation and extinction rates, but each type of data may still provide an incomplete picture of diversification dynamics. Here, we combine species-level palaeontological (fossil occurrences) and neontological (molecular phylogenies) data to estimate deep-time diversity dynamics through process-based birth–death models for Carcharhiniformes, the most speciose shark order today. Despite their abundant fossil record dating back to the Middle Jurassic, only a small fraction of extant carcharhiniform species is recorded as fossils, which impedes relying only on the fossil record to study their recent diversification. Combining fossil and phylogenetic data, we recover a complex evolutionary history for carcharhiniforms, exemplified by several variations in diversification rates with an early low diversity period followed by a Cenozoic radiation. We further reveal a burst of diversification in the last 30 million years, which is partially recorded with fossil data only. We also find that reef expansion and temperature change can explain variations in speciation and extinction through time. These results pinpoint the primordial importance of these environmental variables in the evolution of marine clades. Our study also highlights the benefit of combining the fossil record with phylogenetic data to address macroevolutionary questions.

Mammalian diversification bursts and biotic turnovers are synchronous with Cenozoic geoclimatic events in Asia

Mammalian diversification bursts and biotic turnovers are synchronous with Cenozoic geoclimatic events in Asia

Mammalian diversification bursts and biotic turnovers are synchronous with Cenozoic geoclimatic events in Asia

Asia's rich species diversity has been linked to its Cenozoic geodiversity, including active mountain building and dramatic climatic changes. However, prior studies on the diversification and assembly of Asian faunas have been derived mainly from analyses at taxonomic or geographic scales too limited to offer a comprehensive view of this complex region's biotic evolution. Here, using the class Mammalia, we built historical biogeographic models drawn on phylogenies of 1,543 species occurring across Asia to investigate how and when the mammal diversity in Asian regions and mountain hotspots was assembled. We explore the roles of in situ speciation, colonization, and vicariance and geoclimatic events to explain the buildup of Asia's regional mammal diversity through time. We found that southern Asia has served as the main cradle of Asia's mammal diversity. Present-day species richness in other regions is mainly derived from colonization, but by the Miocene, in situ speciation increased in importance. The high biodiversity present in the mountain hotspots (Himalayas and Hengduan) that flank the Qinghai-Tibetan plateau is a product of high colonization instead of in situ speciation, making them important centers of lineage accumulation. Overall, Neogene was marked by great diversification and migrations across Asia and surrounding continents but Paleogene environments already hosted rich mammal assemblages. Our study revealed that synchronous diversification bursts and biotic turnovers are temporally associated with tectonic events (mountain building, continental collisions) and drastic reorganization of climate (aridification of Asian interior, intensification of Asian monsoons, sea retreat) that took place throughout the Cenozoic in Asia.

Diversification dynamics of chameleons (Chamaeleonidae)

AbstractChameleons are charismatic and common lizards across Madagascar, Africa, and some surrounding regions. Little is known about their diversification dynamics and how this relates to their ecology, so we estimated diversification rate variation and consider this in the context of three hypotheses previously proposed in the literature. First, that the transoceanic dispersal from Africa to Madagascar on two separate occasions has resulted in fast radiation of Malagasy chameleons. Second, that the substantial floral turnover in their distributions within South Africa has resulted in rapid radiations of the endemic dwarf chameleons (Bradypodion). Finally, that the evolution of distinct ecomorphs of chameleon has fuelled fast diversification via adaptive radiations. We use the most recent and complete phylogeny of chameleons to estimate the diversification dynamics of the group using three methods: BAMM (which estimates constant or gradually changing diversification regimes and tests for shifts in these), MEDUSA (which tests for rate shifts in particular clades), and ClaDS (which estimates branch‐specific diversification rates). Our results from all analyses estimate a diversification rate increase in a clade containing most of the genusBradypodion, a group containing the South African dwarf chameleons which occur in recognized biodiversity hotspots in diverse habitats. We find no evidence for shifts resulting from dispersal events to Madagascar or related to the strong ecomorphological divergence of short‐tailed chameleon lineages (Brookesia,Palleon,Rhampholeon, andRieppeleon). The single burst of diversification within chameleons was in a clade which was associated with geographic areas which have experienced rapid habitat turnover and vicariance over the last ~10 million years. This suggests that ‘habitat vicariance’ resulting from ecological changes in vegetation has contributed to the diversity of species in this area by increasing diversification rates.

Resolution, conflict and rate shifts: insights from a densely sampled plastome phylogeny for Rhododendron (Ericaceae).

Rhododendron is a species-rich and taxonomically challenging genus due to recent adaptive radiation and frequent hybridization. A well-resolved phylogenetic tree would help to understand the diverse history of Rhododendron in the Himalaya-Hengduan Mountains where the genus is most diverse. We reconstructed the phylogeny based on plastid genomes with broad taxon sampling, covering 161 species representing all eight subgenera and all 12 sections, including ~45 % of the Rhododendron species native to the Himalaya-Hengduan Mountains. We compared this phylogeny with nuclear phylogenies to elucidate reticulate evolutionary events and clarify relationships at all levels within the genus. We also estimated the timing and diversification history of Rhododendron, especially the two species-rich subgenera Rhododendron and Hymenanthes that comprise >90 % of Rhododendron species in the Himalaya-Hengduan Mountains. The full plastid dataset produced a well-resolved and supported phylogeny of Rhododendron. We identified 13 clades that were almost always monophyletic across all published phylogenies. The conflicts between nuclear and plastid phylogenies suggested strongly that reticulation events may have occurred in the deep lineage history of the genus. Within Rhododendron, subgenus Therorhodion diverged first at 56 Mya, then a burst of diversification occurred from 23.8 to 17.6 Mya, generating ten lineages among the component 12 clades of core Rhododendron. Diversification in subgenus Rhododendron accelerated c. 16.6 Mya and then became fairly continuous. Conversely, Hymenanthes diversification was slow at first, then accelerated very rapidly around 5 Mya. In the Himalaya-Hengduan Mountains, subgenus Rhododendron contained one major clade adapted to high altitudes and another to low altitudes, whereas most clades in Hymenanthes contained both low- and high-altitude species, indicating greater ecological plasticity during its diversification. The 13 clades proposed here may help to identify specific ancient hybridization events. This study will help to establish a stable and reliable taxonomic framework for Rhododendron, and provides insight into what drove its diversification and ecological adaption. Denser sampling of taxa, examining both organelle and nuclear genomes, is needed to better understand the divergence and diversification history of Rhododendron.

Recent divergence in functional traits affects rates of speciation in the Neotropical Velloziaceae (Pandanales)

AbstractThe resurrection plant family Velloziaceae are an iconic element in the Brazilian campos rupestres, where Barbacenia and Vellozia have undergone episodes of explosive species accumulation. Here we focus on the patterns of evolution of growth forms, dry-season physiological strategies and morphofunctional divergence to untangle these radiations. The timings of marked ‘disparification’ (evolution of trait disparity throughout a clade) in both genera were uncoupled from the shifts towards increased diversification rates, with the former accumulating during the Plio-Pleistocene (< 5 Mya). Except for growth forms in Vellozia, the traits analysed display convergent evolution in both genera. Morphofunctional diversity is lower in Barbacenia than in Vellozia, reflecting a young radiation occurring mostly in the southern Espinhaço Province. Growth-form divergence in Vellozia coincided with the Oligocene/Miocene burst in diversification, followed by a slowdown in rate. Moreover, the recent morphofunctional disparification indicates pulses of trait divergence within a mature radiation. Both growth form and divergence in functional traits affect diversification rates in the genera, with the growth forms displaying fastest diversification usually associated with mountain radiations.

Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi.

Whole genome sequences are beginning to revolutionize our understanding of phylogenetic relationships. Yet, even whole genome sequences can fail to resolve the evolutionary history of the most rapidly radiating lineages, where incomplete lineage sorting, standing genetic variation, introgression, and other factors obscure the phylogenetic history of the group. To overcome such challenges, one emerging strategy is to integrate results across different methods. Most such approaches have been implemented on reduced representation genomic data sets, but whole genomes should provide the maximum possible evidence approach. Here, we test the ability of single nucleotide polymorphisms extracted from whole genome resequencing data, implemented in an integrative genomic approach, to resolve key nodes in the phylogeny of the mbuna, rock-dwelling cichlid fishes of Lake Malaŵi, which epitomize the phylogenetic intractability that often accompanies explosive lineage diversification. This monophyletic radiation has diversified at an unparalleled rate into several hundred species in less than 2 million years. Using an array of phylogenomic methods, we consistently recovered four major clades of mbuna, but a large basal polytomy among them. Although introgression between clades apparently contributed to the challenge of phylogenetic reconstruction, reduction of the data set to nonintrogressed sites still did not help to resolve the basal polytomy. On the other hand, relationships among six congeneric species pairs were resolved without ambiguity, even in one case where existing data led us to predict that resolution would be difficult. We conclude that the bursts of diversification at the earliest stages of the mbuna radiation may be phylogenetically unresolvable, but other regions of the tree are phylogenetically clearly supported. Integration of multiple phylogenomic approaches will continue to increase confidence in relationships inferred from these and other whole-genome data sets. [Incomplete lineage sorting; introgression; linkage disequilibrium; multispecies coalescence; rapid radiation; soft polytomy.]

Rapid radiation in a highly diverse marine environment

Rapid diversification is often observed when founding species invade isolated or newly formed habitats that provide ecological opportunity for adaptive radiation. However, most of the Earth's diversity arose in diverse environments where ecological opportunities appear to be more constrained. Here, we present a striking example of a rapid radiation in a highly diverse marine habitat. The hamlets, a group of reef fishes from the wider Caribbean, have radiated into a stunning diversity of color patterns but show low divergence across other ecological axes. Although the hamlet lineage is ∼26 My old, the radiation appears to have occurred within the last 10,000 generations in a burst of diversification that ranks among the fastest in fishes. As such, the hamlets provide a compelling backdrop to uncover the genomic elements associated with phenotypic diversification and an excellent opportunity to build a broader comparative framework for understanding the drivers of adaptive radiation. The analysis of 170 genomes suggests that color pattern diversity is generated by different combinations of alleles at a few large-effect loci. Such a modular genomic architecture of diversification has been documented before in Heliconius butterflies, capuchino finches, and munia finches, three other tropical radiations that took place in highly diverse and complex environments. The hamlet radiation also occurred in a context of high effective population size, which is typical of marine populations. This allows for the accumulation of new variants through mutation and the retention of ancestral genetic variation, both of which appear to be important in this radiation.

Explosive Cenozoic radiation and diversity-dependent diversification dynamics shaped the evolution of Australian skipper butterflies

AbstractAustralia was predominantly tropical for most of the Early Cenozoic, then transitioned to a cooler and drier climate in the Oligocene. In response to this increasing aridity, some lineages either adapted to xeric ecosystems, contracted to increasingly fragmented mesic refugia, or went extinct. However, the lack of macroevolutionary studies at a continental scale precludes a better understanding of Australian biodiversity patterns and processes during the Cenozoic. Here, we infer a robust, dated phylogenomic tree for a radiation of Australian endemic butterflies, the Trapezitinae skippers, to test the impact of biotic and abiotic drivers on Cenozoic diversification dynamics in Australia. These butterflies originated during the Eocene (c. 42 Mya) in the mesic biome of Australia. Trapezitinae exploded in diversity during a cool, dry period in the Late Oligocene and Early Miocene, then experienced a sharp deceleration in speciation. Xeric ecosystems appear to have been colonized more recently, supporting the hypothesis of arid and semi-arid biomes as evolutionary sinks. Temperature-dependent and phytophagy-dependent diversification models received little support. Instead, we find evidence for diversity-dependent processes with declining diversification in Trapezitinae likely linked to limited ecological opportunities following a rapid initial burst of diversification.

Ancient volcanos as species pumps: A case study of freshwater amphipods in Northeast Asia.

Volcano-tectonic processes have been viewed as primary drivers in the formation of present-day diversity. Volcanos associated with mountain uplifts drive allopatric speciation through vicariance and may impact the surrounding areas like species pump or species attractor. However, the application of these hypotheses to aquatic fauna has rarely been tested explicitly. We tested these hypotheses in the Changbai Mountains (Mts), which are one of the most typical, active volcanic ranges in Northeast (NE) Asia with a long and turbulent geological history. The Gammarus nekkensis species complex of amphipod crustaceans, widely distributed throughout NE Asia with poor dispersal abilities and a long evolutionary history, is a suitable model for testing hypotheses of species pump or species attractor. Phylogenetic and ancestral range reconstructions demonstrated that the studied amphipod originated from the Changbai Mts ~27Ma and diverged into eastern (Clade I) and western (Clade II) clades, which corresponds well with the initial volcanic eruption of the Changbai Mts in the Late Oligocene. The subsequent diversifications of subclades CI-3, CII-1a and CII-2a were probably driven by second and third eruptions of the Changbai Mts during the Miocene. In particular, the Changbai lineages had spread to the Russian Far East multiple times since the Early Miocene, and widely colonized the region during the Pleistocene. Our discoveries suggest that the ancient volcanos of the Changbai Mts act as species pumps in NE Asia, resulted in burst of diversification around the Changbai Mts and subsequent dispersals into adjacent regions.

Phylogenomics and biogeography of Cunoniaceae (Oxalidales) with complete generic sampling and taxonomic realignments.

PremiseCunoniaceae are a family of shrubs and trees with 27 genera and ca. 335 species, mostly confined to tropical and wet temperate zones of the southern hemisphere. There are several known issues regarding generic limits, and the family also displays a number of intriguing long‐range disjunctions.MethodsWe performed a phylogenomic study using the universal Angiosperms353 probe set for targeted sequence capture. We sampled 37 species covering all genera in the Cunoniaceae, and those in the three closely related families of the crown Oxalidales (Brunelliaceae, Cephalotaceae, and Elaeocarpaceae). We also performed analyses for molecular dating and ancestral area reconstruction.ResultsWe recovered the topology (Cunoniaceae, (Cephalotaceae, (Brunelliaceae, Elaeocarpaceae))) and a well‐resolved genus‐level phylogeny of Cunoniaceae with strongly supported clades corresponding to all previously recognized tribes. As previously suspected, the genera Ackama and Weinmannia were recovered as paraphyletic. Australasia was inferred as the likely ancestral area for the family.ConclusionsThe current distribution of Cunoniaceae is best explained by long‐distance dispersal with a few possible cases of Australasian–American vicariance events. Extinctions may have been important in determining the mostly Oceanian distribution of this family while some genera in the tribe Cunonieae and in New Caledonia have undergone recent bursts of diversification. New generic diagnoses, 80 new combinations, and one new name are provided for a recircumscribed Ackama (including Spiraeopsis), a much smaller Weinmannia (mostly New World), and a resurrected Pterophylla to accommodate Old World taxa previously in Weinmannia.

Multi-character taxonomic review, systematics, and biogeography of the Black-capped/Tawny-bellied Screech Owl (emMegascops/em ematricapilla/em-emM. watsonii/em) complex (Aves: Strigidae).

Megascops is the most species-rich owl genus in the New World, with 21 species currently recognized. Phylogenetic relationships within this genus are notoriously difficult to establish due to the considerable plumage similarity among species and polymorphism within species. Previous studies have suggested that the widespread lowland Amazonian M. watsonii might include more than one species, and that the Atlantic Forest endemic M. atricapilla is closely related to the M. watsonii complex, but these relationships are as yet poorly understood. A recently published phylogeny of Megascops demonstrated that M. watsonii is paraphyletic with respect to M. atricapilla and that genetic divergences among some populations of M. watsonii are equal to or surpass the degree of differentiation between some M. watsonii and M. atricapilla. To shed light on the taxonomic status of these species and populations within them, we conducted a multi-character study based on molecular, morphological, and vocal characters. We sequenced three mitochondrial (cytb, CO1 and ND2) and three nuclear genes (BF5, CHD and MUSK) for 49 specimens, covering most of the geographic ranges of M. watsonii and M. atricapilla, and used these sequences to estimate phylogenies under alternative Bayesian, Maximum Likelihood, and multilocus coalescent species tree approaches. We studied 252 specimens and vocal parameters from 83 recordings belonging to 65 individuals, distributed throughout the ranges of M. watsonii and M. atricapilla. We used Discriminant Function Analysis (DFA) to analyze both morphometric and vocal data, and a pairwise diagnostic test to evaluate the significance of vocal differences between distinct genetic lineages. Phylogenetic analyses consistently recovered six statistically well-supported clades whose relationships are not entirely in agreement with currently recognized species limits in M. watsonii and M. atricapilla. Morphometric analyses did not detect significant differences among clades. High plumage variation among individuals within clades was usually associated with the presence of two or more color morphs. By contrast, vocal analyses detected significant differentiation among some clades but considerable overlap among others, with some lineages (particularly the most widespread one) exhibiting significant regional variation. The combined results allow for a redefinition of species limits in both M. watsonii and M. atricapilla, with the recognition of four additional species, two of which we describe here as new. We estimated most cladogenesis in the Megascops atricapilla-M. watsonii complex as having taken place during the Plio-Pleistocene, with the development of the modern Amazonian and São Francisco drainages and the expansion and retraction of forest biomes during interglacial and glacial periods as likely events accounting for this relatively recent burst of diversification.

Phylogenetics of mud snakes (Squamata: Serpentes: Homalopsidae): A paradox of both undescribed diversity and taxonomic inflation

Mud snakes (Serpentes: Homalopsidae) are a family of 55 described, mainly aquatic, species primarily distributed throughout mainland Southeast Asia and the Indo-Australian Archipelago. Although they have been the focus of prior research, the basic relationships amongst genera and species remain poorly known. We used a combined mitochondrial and nuclear gene dataset to infer their phylogenetic relationships, using the highest levels of taxon and geographic sampling for any homalopsid phylogeny to date (62% generic and 62% species coverage; 140 individuals). Our results recover two reciprocally monophyletic groups: the fangless Brachyorrhos and its sister clade comprised of all rear-fanged homalopsids. Most genera and interspecific relationships were monophyletic and strongly supported, but intergeneric relationships and intraspecific population structure lack support. We find evidence of both undescribed diversity as well as cases of taxonomic inflation within several species. Tree-based species delimitation approaches (mPTP) support potential new candidate species as distinct from their conspecifics and also suggest that many named taxa may not be distinct species. Divergence date estimation and lineage-through-time analyses indicate lower levels of speciation in the Eocene, with a subsequent burst in diversification in the Miocene. Homalopsids may have diversified most rapidly during the Pliocene and Pleistocene, possibly in relation to tectonic shifts and sea-level fluctuations that took place in Sundaland and the Sahul Shelf. Our analyses provide new insights on homalopsid taxonomy, a baseline phylogeny for the family, and further biogeographic implications demonstrating how dynamic tectonics and Quaternary sea level changes may have shaped a widespread, diverse family of snakes.

Phylogeny and diversification of the gallopheasants (Aves: Galliformes): Testing roles of sexual selection and environmental niche divergence

AbstractThe gallopheasants comprise a clade of 22 species including some of the most elaborately plumaged and highly ornamented birds in the world. They also occupy a remarkable breath of environments and habitats, ranging from lowland rainforests to high grasslands and steppes of the Tibetan plateau. Here, we provide the first well‐resolved species phylogeny of this charismatic group, inferred from ultraconserved elements, nuclear introns and mitochondrial DNA sequences. Unlike previous studies which found unresolvable relationships and suggested a rapid initial burst of diversification, we identified a well‐resolved phylogeny supported in both concatenated and coalescent analytical frameworks, and a steady accrual of lineages through time. Morphological trait reconstructions demonstrated strong phylogenetic signal, not only for highly ornamented males, but also in more cryptically plumaged females. Environmental niche similarly exhibited strong phylogenetic signal. Moreover, evolution of male traits, female traits and environmental niche were all significantly correlated, making it difficult to disentangle their individual roles in gallopheasant diversification.