Search

Speciation is a continuous process driven by barriers to gene flow. Based on genome‐wide SNPs (single nucleotide polymorphisms) of 190 toads from 31 sampling sites of Scutiger boulengeri complex, we found evidence for monophyly which represented a continuous speciation process of at least six lineages in S. boulengeri, which radiated and exhibited varying degrees of divergence and gene flow. The SNP‐based phylogenetic tree was largely discordant with the multilocus mitochondrial tree (i.e., S. mammatus and S. glandulatus nested in the lineages of S. boulengeri) published before. The Min Mountains (MM) and Qinghai‐Tibet Plateau (QTP) lineages differ fundamentally in habitat (i.e., elevation) and morphology (i.e., SVL), we detected signatures of potential high‐altitude and cold adaptation genes in QTP (vs. MM). We found the evidence of reproductive trait disparity (i.e., SVL and nuptial pads) is key to promoting sympatric rather than allopatric species pairs. In addition, we identified selection signals for genes related to sympatric character displacement, genes linked to obesity‐related traits, nuptial spines morphology and enlarged chest nuptial pads in S. mammatus (vs. QTP group of S. boulengeri). Our study provided new insight and paradigm for a varied speciation pattern from local adaptation of allopatry to sympatric character displacement in the S. boulengeri complex. [ABSTRACT FROM AUTHOR]

Sperm morphology varies considerably among species. Sperm traits may contribute to speciation if they diverge fast in allopatry and cause conspecific sperm precedence upon secondary contact. However, their role in driving prezygotic isolation has been poorly investigated. Here we test the hypothesis that, early in the speciation process, female promiscuity promotes a reduction in overlap in sperm length distributions among songbird populations. We assembled a data set of 20 pairs of populations with known sperm length distributions, a published estimate of divergence time, and an index of female promiscuity derived from extrapair paternity rates or relative testis size. We found that sperm length distributions diverged more rapidly in more promiscuous species. Faster divergence between sperm length distributions was caused by the lower variance in the trait in more promiscuous species, and not by faster divergence of the mean sperm lengths. The reduced variance is presumably due to stronger stabilizing selection on sperm length mediated by sperm competition. If divergent sperm length optima in allopatry causes conspecific sperm precedence in sympatry, which remains to be shown empirically, female promiscuity may promote prezygotic isolation, and rapid speciation in songbirds. [ABSTRACT FROM AUTHOR]

The isolated river drainages of eastern North America serve as a natural laboratory to investigate the roles of allopatry and secondary contact in the evolutionary trajectories of recently diverged lineages. Drainage divides facilitate allopatric speciation, but due to their sensitivity to climatic and geomorphological changes, neighboring rivers frequently coalesce, creating recurrent opportunities of isolation and contact throughout the history of aquatic lineages. The freshwater mussel Quadrula quadrula is widely distributed across isolated rivers of eastern North America and possesses high phenotypic and molecular variation across its range. We integrate sequence data from three genomes, including female‐ and male‐inherited mitochondrial markers and thousands of nuclear encoded SNPs with morphology and geography to illuminate the group's divergence history. Across contemporary isolated rivers, we found continuums of molecular and morphological variation, following a pattern of isolation by distance. In contact zones, hybridization was frequent with no apparent fitness consequences, as advanced hybrids were common. Accordingly, we recognize Q. quadrula as a single cohesive species with subspecific variation (Q. quadrula rumphiana). Demographic modeling and divergence dating supported a divergence history characterized by allopatric vicariance followed by secondary contact, likely driven by river rearrangements and Pleistocene glacial cycles. Despite clinal range‐wide variation and hybridization in contact zones, the process‐based species delimitation tool delimitR, which considers demographic scenarios like secondary contact, supported the delimitation of the maximum number of species tested. As such, when interpreting species delimitation results, we suggest careful consideration of spatial sampling and subsequent geographic patterns of biological variation, particularly for wide‐ranging taxa. [ABSTRACT FROM AUTHOR]

Aim: The aim of this study is to infer the geographic dispersal paths and the environmental conditions that shaped the historical biogeography of Brachistosternus scorpions in South America. We evaluated the role that altitude and aridity had on the geographic distance that each species dispersed from the location of the genus common ancestor. Based on the previous studies, we evaluated the hypothesis postulating that species geographic expansion was promoted by arid conditions in high altitudes. Location: South America. Taxon: Brachistosternus genus. Methods: We integrated two methodological approaches in this study, the phylogenetic Geographical model and the Conductance model, considering the uncertainty associated with the phylogenetic relationship and the species classification. The Geo model infers the locations of ancestral species in a phylogenetic tree, assuming a spherical space and using samples of georeferenced locations for every species as input data. It allows us to estimate the species dispersal routes and distances from the location of the genus common ancestor. The Conductance model is based on the circuit theory and infers the geographic route and distance of least resistance between an origin and destination point. We defined the origin as the location of the genus common ancestor obtained from the Geo model and a destination point as the current geographic location of each species. This model infers the geographic routes with the least cost of resistance for dispersal in a landscape of varying altitude and aridity. Finally, we evaluated the correlation between the two dispersal distances each species have moved from the location of the common ancestor, that is, the distance inferred from the Geo model and from the Conductance model. Results: The Geo model shows that Brachistosternus's geographical origin was most likely along the coast of south Peru, and central Chile. From this location, extant species dispersed thorough routes ranging from 873 to 2800 km in average. The Conductance model that considers the routes with least resistance to elevation and aridity simulated dispersal distances that are highly correlated with the species dispersal distances obtained from the Geo model. Main Conclusions: We revealed the geographic dispersal routes, with the least resistance to the pressures imposed by changes in altitude and aridity, that 55 species of scorpions have probably followed in the last 30 million years in South America. These geographic routes that went along the Andean Mountains and the arid zones of South America shaped the current spatial distribution of the genus Brachistosternus. [ABSTRACT FROM AUTHOR]

Aim: Amphiamerican New World fishes provide a unique opportunity to explore the impact of geological processes and the formation of geographic barriers on biological diversification across both spatial and temporal dimensions. We employed phylogenetic and biogeographic methods to assess the impact of the emergence of the Isthmus of Panama on the evolutionary history of snooks. Location: Eastern tropical Pacific and western Atlantic Oceans. Methods: Bayesian methods were used for phylogenetic inference and divergence time estimation, incorporating the fossil record of Carangidae, Centropomidae, Istiophoriformes, Latidae and Sphyraenidae to establish a timeline using the methods of stratigraphic intervals for node calibration density specification. Biogeographic models were fitted to test the hypothesis that transisthmian vicariant events are coeval with the Isthmus closure. To estimate ancestral range probability and perform stochastic mapping, we utilised BioGeoBears and the parameters from the best‐fitting model. This allowed us to estimate the quantity and kind of biogeographical events. Results: Our results suggest a sister relationship between Centropomidae and Sphyraenidae with a common ancestor that originated in the Upper Cretaceous (~78.51 Ma). The biogeographic model BAYAreaLIKE + j indicated speciation in sympatry and dispersal (founder effect) as the primary modes of speciation in the genus Centropomus. The dispersion in the family Centropomidae was estimated from the Tropical Eastern Pacific to the tropical western Atlantic since the Oligocene. Main Conclusions: The alignment of divergence times with ancestral species distributions suggests a possible synchrony between the current distribution in Centropomus species and the processes of the formation of the Isthmus of Panama during the Miocene. However, the evidence of only two transisthmic pair suggests that this event was not determinant in allopatric interbasin speciation. Furthermore, recent diversification events within each basin imply an influence of post‐closure environmental conditions on the evolution of this group of fishes. [ABSTRACT FROM AUTHOR]

ABSTRACT Aim Location Taxon Methods Results Main Conclusions We assess the systematic relationships and historical biogeographic patterns in the subfamily Scincinae, a group of lizards that primarily inhabits the Afro‐Madagascan and Saharo‐Arabian regions with isolated lineages in Europe, North America, East Asia, India and Sri Lanka. The contemporary distribution of these lineages on the historical Laurasian and Gondwanan landmasses make scincines an ideal system to study the roles of vicariance and dispersal on a geologic scale of tens of millions of years.Global.Subfamily Scincinae (Family Scincidae).We conducted biogeographic analyses on a reconstructed, time‐calibrated species tree of scincine genera, including members of the other Scincidae subfamilies, using seven nuclear loci (~6 k base pairs). We also constructed a lineage‐through‐time plot to assess the timing of diversification within scincines.Our analysis estimated strong support for the monophyly of Scincinae that is further comprised a strongly‐supported Gondwanan clade nested within a broader Laurasian group. While most of the extant, genus‐level diversity within the Gondwanan clade was accrued post‐Eocene, the majority of the Laurasian lineages diverged during the Palaeocene or earlier, suggesting large‐scale extinctions on continents of Laurasian origin. Counterintuitively, scincines from India and Sri Lanka have distinct biogeographical origins despite a long tectonic association between these landmasses, suggesting at least two independent, long‐distance, trans‐oceanic dispersal events into the subcontinent. Our biogeographic analyses suggest that scincines likely originated in East and Southeast Asia during the late Cretaceous (ca. 70 Ma), and eventually dispersed westwards to Africa and Madagascar, where their greatest current‐day species richness occurs.Our study demonstrates the concomitant roles of dispersal and extinction in shaping modern‐day assemblages of ancient clades such as scincine lizards. Our range evolution analysis shows that despite the greater diversity observed in the Afro‐Madagascan region, the origin of scincines can be traced back to Southeast Asia and East Asia, followed by westward dispersals. These dispersals may have been followed by significant extinctions in tropical East Asia, resulting in relatively lower diversity of scincines in these regions. Notably, our analysis reveals that Sri Lankan and Peninsular Indian scincines have distinct evolutionary origins. [ABSTRACT FROM AUTHOR]

The relationships of Guiana Shield members of Trichomycterus are examined using three mitochondrial genes (Cytochrome Oxidase 1, Cytochrome b, and 16s) and one nuclear gene (RAG 2). A time-calibrated phylogeny is implemented to examine how diversification is related to the timing of major geographical events in the Guiana Shield. There was topological discordance among the gene trees; however, they overall suggest the presence of two subclades. The T. guianensis subclade consists of the strongly supported relationships of T. sp. 'Potaro, elongate' (Potaro R.) sister to T. guianensis (Potaro R.) + T. sp. 'Ireng, spotted' (Ireng R.). The T. cf. guianensis subclade consists of the strongly supported sister group relationship of T. cf. guianensis (Mazaruni, Potaro, and potentially Caroni Rivers) + T. sp. 'Mazaruni, plain' (Mazaruni R.). Weakly supported as sister to this is T. sp. 'Kusad Mountain' (Takutu R.), and sister to all other members of the subclade is T. conradi (Ireng and Potaro Rivers). The dated phylogeny suggests that the Guiana Shield clade is derived from a lowland ancestor that entered the Proto-Berbice and/or Proto-Essequibo Rivers ∼17.4 Ma. The Proto-Berbice contained the lowland portions of the Ireng and Takutu Rivers, and the Proto-Essequibo contained the lowland portions of the Potaro and Mazaruni Rivers, but the histories of the upland portions of the Ireng, Potaro, and Mazaruni Rivers are less clear and have been thought to have drained northward in what we are referring to as the Grand Pakaraima River in which all members of the T. guianensis clade (except for T. sp. 'Kusad Mountain' and possibly T. conradi) were found. We interpret two geodispersal events into the Grand Pakaraima River and a potential vicariance event ∼9.4 Ma between uplands and lowlands. The likely formation of the modern Guiana Shield rivers occurred 3.8–1.9 Ma, with the modern Ireng River being captured first by the Proto-Essequibo ∼3.8 Ma and finally consolidated ∼1.9 Ma when captured by the Rio Branco. [ABSTRACT FROM AUTHOR]

Recognizing cryptic species is crucial for understanding global biodiversity. The intertidal snail Littoraria flammea is potentially a cryptic species of L. melanostoma widely distributed in the Northwest Pacific. However, the evidence from traditional morphology and single genetic markers is inconsistent. Our study combined quantitative morphological and whole‐genome molecular data to clarify the phylogenetic relationship of three species (L. flammea, L. aff. melanostoma, and L. melanostoma). Three‐dimensional models of shells revealed significant differences in morphology between L. flammea and L. melanostoma. Neutral SNPs indicated that individuals of L. flammea and L. melanostoma were in different clusters. The ratio of interspecific FST to intraspecific FST between L. flammea and L. melanostoma (16) was much larger than the lowest ratio (2.31) in six published genera with cryptic species in gastropods. Non‐neutral SNPs disclosed divergence in functional genes related to reproduction and protein binding. The morphological and phylogenetic analyses corroborated the transitional status of L. aff. melanostoma. These results confirmed that the L. flammea snails north of the Yangtze River Estuary is a cryptic species of L. melanostoma, and allopatric speciation occurs in the L. melanostoma complex. [ABSTRACT FROM AUTHOR]

Recent studies have proposed different biogeographic patterns of intertidal Diaulota and marine littoral Psammostiba along the Pacific coasts of the Northern Hemisphere. To compare the biogeographic patterns of different lineages of aleocharine beetles and explore the recurrent patterns among them, we studied coastal Adota , with a distribution range almost identical to those of Diaulota and Psammostiba. We performed phylogenetic analysis of the marine littoral Adota occurring on the Pacific coasts of the Northern Hemisphere using molecular characters (5188 bp: ~1452 bp of COI , ~404 bp of COII , ~475 bp of 16S , ~879 bp of 18S , ~973 bp of 28S , ~542 bp of EF1-α and ~463 bp of Wg) to discuss their phylogenetic relationships and biogeographic patterns. The data were analysed using parsimony (PA), Bayesian (BA) and maximum likelihood (ML) methods. The genus Adota and clade A with the same patterns of relationships (A. sinanensis ((A. elongata + A. koreana) (A. magnipennis + A. ushio))), were strongly supported as monophyletic in all analyses. The PA, BA and ML analyses yielded different species relationships in clade B: (A. kamchatkaensis (A. namhae + A. maritima)) in the ML tree using IQ-TREE2 , (A. namhae (A. kamchatkaensis + A. maritima)) in the BA and RAxML trees and unresolved polytomy in the PA tree. Our results suggest that the ancestors of Adota were widespread along the East Asian coasts (North and South Korea, Japan, and Kamchatka, Russia). Subsequently, Adota species expanded their range and underwent vicariance between South Korea and Japan and Russia (Kamchatka). Later, another dispersal event occurred from South Korea and Japan to North America and a vicariance event occurred between South Korea and Japan, and North America. Adota have similar biogeographical patterns to Psammostiba , probably because they occupy the same microhabitats and have similar biological characteristics. The findings demonstrate the importance of microhabitats and biological traits in the study of biogeographic patterns of marine coastal insects. Here, we present the results of the first phylogenetic and biogeographical analysis of the marine littoral Adota on the Pacific coasts of the Northern Hemisphere. The biogeographic patterns were compared with those of different lineages of aleocharine beetles with different microhabitats. Reconstructions of the ancestral areas suggest that the common ancestor of Adota occurred widely along the East Asian coasts. Both dispersal and vicariance were important in shaping the current distribution. (Image credit: Jong-Keun Jung and Kee-Jeong Ahn.) [ABSTRACT FROM AUTHOR]

The biota of the Indian subcontinent is a result of Gondwanan vicariance to some extent but largely through multiple faunal exchanges between neighbouring regions. However, in recent times, humans have influenced regional biotas through the human-mediated transport of many generalist species. In this study, we report populations of Lankascincus fallax, a skink species supposedly endemic to Sri Lanka, from the west coast of Kerala in India. We conducted morphological and genetic analysis to ascertain the identity of this species and to check whether the Indian population is monophyletic. We then performed a divergence dating analysis to test whether the presence of this population is a result of ancient dispersal into India or a result of more recent events. Additionally, we used species distribution modelling to test whether the Indian L. fallax is a result of natural dispersal into India during the past (mid-Pliocene to the last glacial maximum) when there were possible land bridges between India and Sri Lanka. We find that the Indian population is nested within the Sri Lankan L. fallax and that this population diverged from the Sri Lankan population very recently, during the Pleistocene. We do not find climatic suitability between the Indian west coast and Sri Lanka under current climatic conditions, or during the past suggesting no suitable dispersal corridors between India and Sri Lanka. Overall, we hypothesize that the Indian populations of L. fallax are likely a result of human-mediated transport into India and subsequent dispersal across the west coast of Kerala. [ABSTRACT FROM AUTHOR]

Cryptic species complexes consist of geographically confluent, closely related species that were once classified as a single species. The diversification mechanisms of cryptic species complexes often are mediated by environmental factors, which in some cases lead to ecological speciation. Niche-based distribution modeling can be an important tool in characterizing the extent of ecological divergence between species that may have resulted from environmentally driven speciation scenarios. We used climatic niche modeling to examine the degree of ecological divergence within the Paragalago zanzibaricus species complex in East Africa. We expected parapatrically distributed P. cocos and P. zanzibaricus to display a significant degree of climatic niche distinction and allopatrically distributed P. zanzibaricus and P. granti to exhibit a degree of niche conservatism. The extent of niche overlap between the three species was assessed by using a Niche Similarity Analysis (NSA) on bioclimatic values. Selected models for all three species exhibited good predictive ability, although the model for P. cocos was most optimal and appeared most consistent with its known range. NSA showed that P. cocos and P. zanzibaricus were statistically more similar than predicted from null distributional values. Results for NSA between the other two species pairings appear to be within the null distribution. The extent of niche overlap between all three species is consistent with the expectations of allopatric speciation processes. Future studies should examine alternative hypotheses for speciation within this group, including the role of sensory drive, interspecific competition, and the impact of Plio-Pleistocene climatic cycles. [ABSTRACT FROM AUTHOR]

Aim: Species with disjunct geographic distributions provide natural opportunities to investigate incipient or recent allopatric divergence. The combination of both genetic and ecological data may be fruitful to decipher the causes of such patterns: (i) actual vicariance, (ii) successful colonisation from one source to a new range (dispersal, biological introduction) or (iii) parallel convergent evolution. Location: Southern France and Northern Spain. Taxon: The bee orchid Ophrys aveyronensis (and its two recognised subspecies O. a. subsp. aveyronensis and O. a. subsp. vitorica) displays a disjunct geographic distribution with two subranges separated by 600 km on both sides of the Pyrenees mountain range. Methods: As allopatric divergence is often complex to document in the wild, we used a combination of population genomics and ecological niche modelling (ENM) to investigate the causes of this intriguing biogeographic pattern. Results: The population genomic data demonstrate that all the studied populations exhibit similar patterns of genetic diversity and dramatic decrease in effective size compared with the ancestral population. Significant genetic differentiation and reciprocal monophyly exist between populations of the two subranges of O. aveyronensis, despite a very recent divergence time as young as ca. 1500 generations ago. Moreover, paleo‐ENM analyses support that the disjunct geographic distribution of O. aveyronensis is consistent with a range split of a broad ancestral range, contraction and distinct longitudinal and latitudinal shifts in response to climate warming during the Holocene. Main Conclusion: The congruence of the results obtained from both population genomics and ENM approaches documents how very recent continental allopatric divergence initiated speciation in this system. O. aveyronensis provides a promising opportunity to study the onset of reproductive isolation and parallel evolution following an initial stage of geographic separation in a group with high diversification rate. [ABSTRACT FROM AUTHOR]

Aim: Scutigeromorpha is a globally distributed, ancient group of centipedes with at least 400 million years of evolutionary history. We assess the biogeographic history of the order, with a particular focus on the Peninsular Indian Plate (PIP), a Gondwanan fragment. We hypothesize that continental vicariance explains the disjunct distribution of extant scutigeromorphs, that PIP scutigeromorphs are of ancient Gondwanan origins, and that East Gondwana vicariance explains the diversification of the subfamily Thereuoneminae into its Asian and Australian clades. Location: Global. Taxa: Centipedes, Scutigeromorpha. Methods: We use a novel molecular dataset sampled across the PIP and a global sequence database representing the geographic distribution of all families and subfamilies. We employ molecular phylogenetic analyses on two mitochondrial and three nuclear markers, molecular species delimitation and ancestral range estimation to reconstruct biogeographic history. Results: Ancestral scutigeromorphs were likely widely distributed across Gondwana and diverged prior to any continental vicariance. Their subsequent biogeography is shaped by continental vicariance, long‐distance dispersal and jump dispersal, indicating an ability to colonize areas far from their ancestral range. The PIP emerged as the ancestral range of Thereuoneminae, which started diversifying during the Cretaceous Period. Subsequent in‐situ diversification within the PIP and dispersals into Asia, Australia and the Pacific Islands best explained the extant distribution of Thereuoneminae, more so than East Gondwana vicariance. Main Conclusions: The in‐situ diversification of PIP species and their ancient divergence suggest they represent Gondwanan relicts in a landmass whose biota is primarily dispersal‐driven. A single dispersal event from the PIP generated most of the extant diversity in Australia, another Gondwanan fragment. Furthermore, the discovery of 11 putative species from the PIP and the Andaman Islands, five times more than was known, highlights the Wallacean and Linnean shortfalls in tropical Asia. [ABSTRACT FROM AUTHOR]

The c. 270 endemic species of Pedicularis in the Himalaya–Hengduan Mountains (HHM) region exhibit high diversity in geographic distribution, elevational range and floral morphology. Many of these, including the species with the longest corolla tubes and beaked galeas, are monophyletic and represent a putative in situ radiation. In this study, we focus on the representative Clade 3 within the HHM region. We integrate the plastid phylogeny of this clade with environmental data and species distributions to infer environmental correlates of species diversity. We estimate macroevolutionary rates and reconstructed ancestral states for geographic ranges and corolla traits, and analyse patterns of range overlap and niche evolution to assess drivers of diversification in the HHM region. Our results show that the region from northwest Yunnan to southwest Sichuan is the centre of diversity for this clade of Pedicularis. Rates of diversification are associated with precipitation and multiple environmental factors. Multiple range expansions from the Sanjiang (Three Parallel Rivers) region, followed by allopatric speciation across the HHM region, contributed to early rapid diversification. Corolla traits are not significantly associated with species diversification. This study highlights the importance of integrated evidence for understanding species diversification dynamics and contributes to our understanding of the origins of the remarkable richness of plant species in the HHM region. [ABSTRACT FROM AUTHOR]

Biogeographers have often been puzzled by several unusual features in the Juan Fernández Islands (JFI) biota. These include the very high endemism density, multiple endemics that are older than the current islands, close biogeographic affinities with the central and West Pacific, and affinities with the diverse Coast Range of central Chile. We review aspects of biogeography in the JFI and the Coast Range in light of recent geological studies. These have examined the mantle below the East Pacific and South America, and have produced radical, new ideas on tectonic history. A long‐lived, intraoceanic archipelago ~9000 km long is now thought to have existed in the East Pacific (passing between the JFI hotspot and mainland Chile) until the mid‐Cretaceous. At this time, South America, which was moving westward with the opening of the Atlantic, collided with the archipelago. The assumption that the JFI biota is no older than its current islands is questionable, as taxa would have survived on prior islands produced at the JFI hotspot. We propose a new interpretation of evolution in the region based on tectonics rather than on island age and incorporating the following factors: the newly described East Pacific Archipelago; a long history for the JFI hotspot; metapopulation dynamics, including metapopulation vicariance; and formation of the Humboldt Current in the Cretaceous. The model accounts for many distinctive features of the JFI and Coast Range biota. [ABSTRACT FROM AUTHOR]

Ctenomys (tuco-tucos) is one of the most speciose genera of mammals, with around 70 described species. Recently, the rate of new species descriptions within the genus Ctenomys has notably increased, primarily due to recent taxonomic revisions and surveys in previously unexplored geographic areas. In this study, utilizing both morphological and molecular evidence, we describe a new species of Ctenomys from northern Argentine Patagonia, confined between the Colorado and Negro rivers. This new species is a member of the Magellanicus group displaying close relationships with other species distributed in northern Patagonia and adjacent regions (C. bidaui, C. miguelchristie, C. pontifex, and C. pulcer). The major rivers in the region (Colorado and Negro rivers) appear to delineate the distributional boundaries of the identified taxa. We therefore propose that rivers, acting as natural barriers to dispersal, have significantly influenced the diversity of Ctenomys in northern extra-Andean Patagonia. [ABSTRACT FROM AUTHOR]

Microbial communities that maintain symbiotic relationships with animals evolve by adapting to the specific environmental niche provided by their host, yet understanding their patterns of speciation remains challenging. Whether bacterial speciation occurs primarily through allopatric or sympatric processes remains an open question. In addition, patterns of DNA transfers, which are pervasive in bacteria, are more constrained in a closed host-gut system. Eusocial bees have co-evolved with their specialized microbiota for over 85 million years, constituting a simple and valuable system to study the complex dynamics of host-associated microbial interactions. Here, we studied the patterns of speciation and evolution of seven specialized gut bacteria from three clades of eusocial bee species: western honey bees, eastern honey bees, and bumblebees. We conducted genomic analyses to infer species delineation relative to the patterns of homologous recombination (HR), and horizontal gene transfer (HGT). The studied bacteria presented various modes of evolution and speciation relative to their hosts, but some trends were consistent across all of them. We observed a clear interruption of HR between bacteria inhabiting different bee hosts, which is consistent with a mechanism of allopatric speciation, but we also identified interruptions of HR within hosts, suggesting recent or ongoing sympatric speciation. In contrast to HR, we observed that HGT events were not constrained by species borders. Overall, our findings show that in host-associated bacterial populations, patterns of HR and HGT have different impacts on speciation patterns, which are driven by both allopatric and sympatric speciation processes. [ABSTRACT FROM AUTHOR]

The study of adaptive radiations has shed light on our current understanding of evolution. However, previous studies examining the mode in which species diversified, how diversification rates varied, and how ecological specialisation affected these processes have found few different results across different taxa and geographic and ecological systems, showing how complex this process is. To gain a more complete picture of how species evolve, additional model systems that encompass alternative ecological requirements are needed. Here, we present the results of a study aimed at unravelling the diversification mode and evolutionary drivers of the spider genus Dysdera, the red devil spiders, endemic to the Canary Islands. These species exhibit remarkable phenotypic variability in their mouthparts, which has been related to different levels of specialisation in the predation of isopods. We explored patterns of lineage diversification and assessed the role of trophic specialisation as a driver of species diversification. Additionally, we used climatic variables, occurrence data and morphological information to unravel the underlying mode of speciation by means of joint species distribution models and age‐range correlation methods. Our results reveal that red devil spiders underwent an early burst of diversification, followed by a slowdown of diversification rates, which is a hallmark of adaptive radiation. We also found evidence that the trophic morphology shaped diversification, with specialist species exhibiting higher rates of diversification. Finally, our analyses suggest that speciation occurred mostly in allopatry, with subsequent secondary sympatry following range expansion. [ABSTRACT FROM AUTHOR]

Plant species diversity may be considerably underestimated, especially in evolutionarily complex genera and in diversity hotspots that have enabled long‐term species persistence and diversification, such as the Balkan Peninsula. Here, we address the topic of underexplored plant diversity and underlying evolutionary and biogeographic processes by investigating the hygrophytic mountain species complex of Cardamine acris s.l. distributed in the Balkans (three subspecies within C. acris) and northwestern Anatolia (C. anatolica). We performed a series of phylogenetic and phylogeographic analyses based on restriction‐site associated DNA sequencing (RADseq) and target enrichment (Hyb‐Seq) data in combination with habitat suitability modelling. We found C. anatolica as a clade nested within the Balkan C. acris, probably resulting from a founder event, and uncovered three allopatric cryptic lineages within C. acris subsp. acris, allowing us to recognise a total of six entities in this complex. We observed the deepest genetic split within C. acris subsp. acris in the western Balkans, which was at odds with taxonomy and showed no distribution gap. We inferred vicariance as the most likely process for population divergence in the Balkans, accompanied by gene flow between the recognised entities, which was consistent with the modelled habitat suitability dynamics. Furthermore, we discovered several polyploid populations in C. acris, representing both pure intra‐ and inter‐lineage hybrid polyploids, but detected only minor traces of hybridization with related congeners. Overall, our results illustrate that diverse evolutionary processes may influence the history of mountain plant species in the Balkan Peninsula, including vicariance, reticulation, polyploidization and cryptic diversification. [ABSTRACT FROM AUTHOR]

The Zambezi grunter, Parauchenoglanis ngamensis , is currently distributed across four (sub)basins in southern and south-central Africa, namely the Okavango, upper Zambezi, Kwanza, and Kasai. The present study used a combination of molecular (barcoding), colour pattern, and other morphological data to explore the possible existence of hidden species diversity within this species. Based on the available samples, analyses of molecular data uncovered seven well-supported (.96–1.00 Bayesian posterior probabilities) candidate species, with 1.6%−8.5% genetic divergence between them. These, in addition to two more candidate species without genetic data, exhibited a combination of consistent colour pattern and other morphological differences that supported their distinction. The present study redescribes P. ngamensis , which is confined to the Okavango and upper Zambezi (sub)basins, and describes eight new species: two from the Kwanza Basin and six from the Kasai sub-basin. The fact that some of the species occur allopatrically, whereas others are sympatric and even syntopic indicates the complex palaeogeographical history of these basins. In addition, the high species diversity discovered in the Kasai sub-basin seems to be related to its highly peculiar hydrography. Accurate delimitation of species boundaries and mapping of their distribution is crucial for conservation assessments and guiding their protection. [ABSTRACT FROM AUTHOR]

The rise of the Isthmus of Panama separated the populations of many marine organisms, which then diverged into new geminate sister species currently living in the Eastern Pacific Ocean and the Caribbean Sea. However, we know very little about how such evolutionary divergences of host species have shaped the compositions of their microbiomes. Here, we compared the microbiomes of whole-body and shell-surface samples of geminate species of marine gastropods in the genera Cerithium and Cerithideopsis to those of congeneric outgroups. Our results suggest that the effects of ~3 million years of separation and isolation on microbiome composition varied among host genera and between sample types within the same hosts. In the whole-body samples, microbiome compositions of geminate species pairs tended to be similar, likely due to host filtering, although the strength of this relationship varied among the two groups and across similarity metrics. Shell-surface microbiomes show contrasting patterns, with co-divergence between the host taxa and a small number of microbial clades evident in Cerithideopsis but not Cerithium. These results suggest that (i) isolation of host populations after the rise of the Isthmus of Panama affected microbiomes of geminate hosts in a complex and host-specific manner, and (ii) host-associated microbial taxa respond differently to vicariance events than the hosts themselves. IMPORTANCE While considerable work has been done on evolutionary divergences of marine species in response to the rise of the Isthmus of Panama, which separated two previously connected oceans, how this event shaped the microbiomes of these marine hosts remains poorly known. Using whole-body and shell-surface microbiomes of closely related gastropod species from opposite sides of the Isthmus, we show that divergences of microbial taxa after the formation of the Isthmus are often not concordant with those of their gastropod hosts. Our results show that evolutionary responses of marine gastropod-associated microbiomes to major environmental perturbations are complex and are shaped more by local environments than host evolutionary history. [ABSTRACT FROM AUTHOR]

A good knowledge of the evolutionary history of organisms and an accurate taxonomic framework are keys for efficient biodiversity conservation measures. This is particularly relevant for European butterflies, which are often used as bioindicator organisms and umbrella species for conservation.The Holarctic butterfly genus Agriades includes seven European arctic‐alpine species of which several have a debated taxonomic status. They are localized and allopatric, and at least two of them are of high conservation concern, namely A. aquilo (in Europe, restricted to northern Scandinavia) and A. zullichi (endemic to southern Spain). Despite high conservation value and taxonomic uncertainty, molecular studies on these taxa are limited to DNA barcodes.We investigated the evolutionary history and species delimitation of West Palearctic Agriades using double‐digest RAD sequencing (ddRADseq).Various analyses using genomic data suggested the presence of one species in the glandon species group and one or two in the pyrenaicus species group. The differentiation within the former group (i.e., glandon, aquilo, zullichi) appears to be relatively recent, although the main allopatric populations represent evolutionary significant units (ESUs). Notable geographic structure was found within the pyrenaicus species group, with four allopatric ESUs detected.Wolbachia screening highlighted the presence of several allele combinations, some associated with particular Agriades populations.Genomic data revealed the evolutionary trajectory of European Agriades and a tendency for taxonomic oversplitting within this genus. These findings aid conservation by providing genetic background for region or population prioritization (including ESUs), and for the management of potential population reinforcement or reintroductions. [ABSTRACT FROM AUTHOR]

Aim: To date a vicariant event through the mutualistic relationship of a hylid frog and its bromeliad host found across two isolated mountain ranges as part of an island–continental split and to use this information to calibrate a molecular dating analysis of hylids. Location: South America. Time Period: Pliocene. Major Taxa Studied: Treefrogs, Arboranae. Methods: Pliocene tectonic movements sank a portion of a mountain range that connected present‐day Trinidad (island) and northern Venezuela, eventually isolating populations of the golden tree frog Phytotriades auratus and its host bromeliad Glomeropitcairnia erectiflora on both sides of a saltwater barrier. We estimated the submersion rate timing of the vicariant event, then employed ecological niche modelling to establish the distribution of the frog and its host to the Pliocene. We generated nucleotide sequence data for the hylid on each side of the marine barrier and proposed a biogeographic calibration for the split between populations. Using Bayesian phylogenetic analysis, we evaluated the impact of incorporating this biogeographic calibration on estimates of treefrog divergence times. Results: A relatively continuous, high‐elevation mountain range existed before the Pliocene and the opening of the Gulf of Paria (4.45 ± 0.85 Ma). Phytotriades auratus and G. erectiflora would have been distributed across the Paria and Northern Range mountains as a single population since the Pliocene. Divergence times among treefrogs (Arboranae) were older than those inferred using fossil calibrations alone, with mean age estimates for subfamilies and genera being ~2 and ~1.2 million years older, respectively. Main Conclusions: Our study presents a biogeographic calibration based on a vicariant model that connects the evolution of the populations of a hylid through geology and ecological data. The implementation of this date as a molecular clock calibration reduces the uncertainty in date estimates for the shallower nodes in the phylogeny of Arboranae. [ABSTRACT FROM AUTHOR]

The North Pacific distribution of coastal aleocharines has been explained as the result of either dispersal or vicariance. The rove beetle genus Psammostiba is a marine littoral group that occurs on the Pacific coasts of the Northern Hemisphere. We performed phylogenetic analysis of Psammostiba using molecular characters (4685 bp) to investigate their biogeographic patterns. The data were analysed using parsimony, Bayesian and maximum likelihood methods. Model‐based analyses showed the same pattern of Psammostiba species relationships, but parsimony analysis yielded different species relationships for the unresolved clade of Psammostiba. According to the reconstruction of the ancestral areas, both vicariance (two events) and dispersal (one event) have played roles in shaping its current distribution. Biogeographical analyses suggest that the common ancestor of Psammostiba occurred widely along the Pacific coasts of the Northern Hemisphere and underwent vicariance events. [ABSTRACT FROM AUTHOR]

The Gesneriaceae consists of around 150 genera and c. 3750 species with a predominantly tropical and subtropical distribution across all continents. Although previous studies have proposed an American origin of Gesneriaceae, the biogeographic history of this pantropical plant family is still unclear, particularly in the Old World. To address this, we assembled the most comprehensively sampled matrix of Gesneriaceae with 143 Gesneriaceae genera and 355 species, including key samples from Sri Lanka analysed here for the first time. We generated molecular phylogenies based on four plastid gene regions (ndhF, matK, rps16 and trnL-F), obtained fossil-calibrated trees, and reconstructed ancestral areas and dispersal routes using Bayesian methods. Our results confirm the origin for the family in the Early Palaeocene (67. Ma) in the region of present day Central America & Andean South America, and that diversity in the Old World originated from a longdistance dispersal event from South America around 59 Ma, most likely to the Indian plate, which was an island at the time. This lineage then dispersed to Malesia and later East Asia, which would ultimately become a major centre of diversity and source of many dispersals to other regions. Our results thus highlight the Indian plate as a likely key player in the early diversification of Old World Gesneriaceae, even though it is now more diverse elsewhere, and hence offer novel insights into this plant family’s dispersal routes and areas of diversification in the Old World.

The progressive aridification of the Australian continent, and coincident decline of mesic forest, has been a powerful driver of allopatric and environmental speciation in native species. The relictual mesic forests of the eastern seaboard now harbour a diverse group of endemic fauna, including the wood‐feeding cockroaches of the genus Panesthia, which reached the continent via two separate invasions from Melanesia. The more recent of these colonization events gave rise to a group of five recognized species, occurring in mainland woodlands, sclerophylls and rainforests, as well as the forests and grasslands of the Lord Howe Island Group. Due to limited sampling in molecular studies and doubt regarding the standing taxonomy, there is little certainty about relationships among the species and poor understanding of the effects of ancient climatic change upon their evolution. We undertook a comprehensive phylogenetic analysis of the clade, using complete mitogenomes and nuclear ribosomal markers from nearly all known morphospecies and populations. Our time‐calibrated phylogenetic analyses reveal an additional six unrecognized, highly divergent lineages and suggest that these have arisen primarily through vicariance as rainforests fragmented during Plio‐Pleistocene glacial cycles (2–5 million years ago). Ancestral niche estimations also evidence a tropical rainforest origin for the group, followed by at least three niche transitions into drier forest, including one associated with the singular colonization of the Lord Howe Island Group. Finally, we find evidence of frequent, parallel wing reduction, in potential association with the contraction of forest habitats into small refugia. Our results reiterate the far‐reaching role of ancient aridification in driving speciation, niche expansion and morphological evolution in Australian fauna. [ABSTRACT FROM AUTHOR]

Under allopatric speciation, populations of a species become isolated by a geographic barrier and develop reproductive isolation through genetic differentiation. When populations meet in secondary contact, the strength of evolved reproductive barriers determines the extent of hybridization and whether the populations will continue to diverge or merge together. The yellowhammer (Emberiza citrinella) and pine bunting (E. leucocephalos) are avian sister species that diverged in allopatry on either side of Eurasia during the Pleistocene glaciations. Though they differ greatly in plumage and form distinct genetic clusters in allopatry, these taxa show negligible mitochondrial DNA differentiation and hybridize extensively where they overlap in central Siberia, lending uncertainty to the state of reproductive isolation in the system. To assess the strength of reproductive barriers between taxa, we examined genomic differentiation across the system. We found that extensive admixture has occurred in sympatry, indicating that reproductive barriers between taxa are weak. We also identified a putative Z chromosome inversion region that underlies plumage variation in the system, with the 'pine bunting' haplotype showing dominance over the 'yellowhammer' haplotype. Our results suggest that yellowhammers and pine buntings are currently at a crossroads and that evolutionary forces may push this system towards either continued differentiation or population merging. However, even if these taxa merge, recombination suppression between putative chromosome Z inversion haplotypes may maintain divergent plumage phenotypes within the system. In this way, our findings highlight the important role hybridization plays in increasing the genetic and phenotypic variation as well as the evolvability of a system. [ABSTRACT FROM AUTHOR]

Background: The ability to predict and comprehend molecular interactions offers significant insights into the biological functions of proteins. The interaction between surface protein 47 of Plasmodium falciparum (Pfs47) and receptor of the protein 47 (P47Rec) has attracted increased attention due to their role in parasite evasion of the mosquito immune system and the concept of geographical coevolution between species. The aims of this study were as follows: to apply a bioinformatics approach to investigate the interaction between Pfs47 and P47Rec proteins and to identify the potential binding sites, protein orientations and receptor specificity sites concerning the geographical origins of the vectors and the parasite. Methods: Public sequences of the pfs47 and p47rec genes were downloaded and subsequently filtered to predict functional and structural annotations of the Pfs47-P47Rec complex. Phylogenetic analyses of both proteins were carried out. In addition, the p47Rec gene was subjected to sequencing and subsequent analysis in 2 distinct Anopheles species collected in Honduras. Results: The examination of motifs reveals a significant degree of conservation in pfs47, suggesting that Pfs47 might have undergone recent evolutionary development and adaptation. Structural models and docking analyses supported the theory of selectivity of Plasmodium falciparum strains towards their vectors in diverse geographical regions. A detailed description of the putative interaction between the Pfs47-P47Rec complex is shown. Conclusions: The study identifies coevolutionary patterns between P47Rec and Pfs47 related to the speciation and geographic dispersion of Anopheles species and Plasmodium falciparum, with Pfs47 evolving more recently than P47Rec. This suggests a link between the parasite's adaptability and existing anopheline species across different regions. P47Rec likely has a cytoplasmic localization due to its lack of membrane attachment elements. However, these findings are based on simulations and require validation through methods like cryo-electron microscopy. A significant limitation is the scarcity of sequences in global databases, which restricts precise interaction modelling. Further research with diverse parasite isolates and anopheline species is recommended to enhance understanding of these proteins' structure and interaction. [ABSTRACT FROM AUTHOR]

Aim: We studied the niche evolution and diversification modes in transisthmian Alpheus shrimps by examining the interplay between environmental niche divergence and conservatism in allopatric sister species. In a broader perspective, the current study analysed the evolution of climatic niche and the role of the environment in species diversification of Alpheus transisthmian shrimp. Location: Atlantic and Eastern‐Pacific oceans. Taxon: Alpheus shrimps (Caridea: Alpheidae). Methods: We assembled georeferenced occurrences for 33 species of Alpheus (with 24 sister species) from a time‐calibrated molecular phylogeny. We modelled their ecological niches and assessed niche overlap through pairwise comparisons. Additionally, we performed phylogenetic reconstructions of the ancestral environmental niche, for each niche axis. Results: Our results demonstrate that thermal tolerances, food availability and hydrodynamic forces were relevant environmental axes in evolutionary processes in transisthmian species of Alpheus. Among the 528 paired comparisons, we found that most niches were divergent, including in 12 clades formed by pairs of sister species (in only two of these clades were the niches fully equivalent). Phylogenetic reconstructions of ancestral niches showed an initial niche conservatism in all axes, with divergences intensifying in the last 12 million years. Main Conclusions: We found evidence that confirms the relevance of the environmental changes that occurred in the West Atlantic and East Pacific for niche evolution in transisthmian Alpheus species, as well as for the emergence of some lineages. Our findings provide evidence for different modes of Alpheus species speciation in a period consistent with the closure of the Isthmus of Panama. [ABSTRACT FROM AUTHOR]

The Palpimanidae are one of five extant Palpimanoidea families that occur mainly in South America and Africa, although there are lineages in Madagascar, islands of the Indian Ocean, and parts of Asia. Here we examine the role of plate tectonics in shaping the distribution of Palpimanidae. We perform molecular sequencing via target enrichment, which makes use of fragmented DNA, because most specimens are stored in natural history museum collections and were not properly preserved for molecular sequencing. We perform phylogenetic analysis, divergence dating, and ancestral range reconstructions to assess whether continental vicariance shaped the evolution of Palpimanidae. We also examine evolution of eye loss via ancestral character reconstruction. We report the first Palpimanidae phylogeny based on genomic data that samples the majority of Chediminae genera. Results suggest that Palpimanidae originated in the Triassic, with diversification spanning the Jurassic to the Cretaceous. Vicarance played a role in early diversification, with later range expansion out of Africa. Based on morphology and phylogenetic analysis, Sceliraptor is synonymized with Sarascelis , Sceliscelis is synonymized with Scelidocteus , and the new genus and species Sitamacho tao gen. nov. sp. nov. is described, with three species transferred from Hybosida. [ABSTRACT FROM AUTHOR]

The genus Carabus (Coleoptera: Carabidae: Carabinae) is a group of predacious ground beetles found throughout Holarctic temperate zones. The diversification of this group is attributed not only to allopatric speciation but also to diversification in life-history traits and morphological traits that are involved in ecological adaptation and reproductive isolation. Precise phylogenetic reconstruction of Carabus is important to understanding the factors associated with species' divergence in relation to such character divergence. Here, we analyse the phylogeny of Carabus among higher taxonomic groups and among species of the subgenus Apotomopterus , a hyper-diverse group endemic to East Asia. We used genome-wide sequence data from ultraconserved elements for phylogenetic reconstruction via maximum-likelihood and species-tree reconstruction methods. With regard to the relationships among higher taxonomic groups, the obtained phylogenetic trees resolved two structures with previously unresolved divergence. The subgenus Apotomopterus contained three lineages, i.e. the Vitalisi, Prodigus, and Sauteri groups. It showed diversification of the spinula, a sclerotized male genital structure, and variation in the female elytral notch (preapical emargination). These morphological traits may be involved in copulatory behaviour and potentially affect reproductive isolation, and their character state divergence may have facilitated species divergence of Apotomopterus. [ABSTRACT FROM AUTHOR]

We analysed phylogenetic relationships within a major clade of Cyprinodontiformes (Teleostei) that includes five families of North American killifishes. We used DNA sequences from five genes for 130 species, with four fossil calibrations and three secondary calibrations, to generate a time-calibrated phylogeny. We estimated diversification rates, ancestral areas, and ancestral habitats for each node. Findings were interpreted within a detailed biogeographical synthesis. The results indicate that the clade arose in the Eocene along the Gulf of México coast. The speciation rate was uniform through time, except for acceleration in Cyprinodontidae after ~10.9 Mya. In other families, neither viviparity nor marine-to-freshwater transition was associated with accelerated speciation. Sea-level fluctuations might have created a speciation pump by stimulating cycles of dispersal and vicariance along the coast. Diversification also included many cases of inland immigration from coastal ancestors. For upland lineages, ancient river drainages accord with lineage distributions, including enigmatic disjunctions in Goodeidae and Fundulus. Diversification in uplands occurred via barrier displacement within alluvial or tectonically active landscapes. Killifishes also display high environmental tolerance and persist within harsh, peripheral environments unsuitable for most other fishes. Hence, a combination of clade antiquity, adaptability, dynamic geography, and persistence can explain the living diversity of New World killifishes. [ABSTRACT FROM AUTHOR]

The North Pacific distribution of coastal staphylinids may be explained as the result of either dispersal or vicariance. The intertidal rove beetle genus Diaulota is a submarine group that occurs on the Pacific coasts of the Northern Hemisphere. We performed a phylogenetic analysis of Diaulota using molecular characters (3241 bp) to investigate their biogeographic history and patterns. The data were analysed by parsimony, Bayesian, and maximum likelihood methods. Model-based analyses showed the same pattern of Diaulota species relationships, but parsimony analysis resulted in different species relationships for the unresolved clade B. Biogeographical analyses suggested that the common ancestor of Diaulota occurred widely along the East Asian coast with repeated dispersal to the north-eastern Pacific from the north-western Pacific. According to the reconstruction of the ancestral areas, both dispersal (seven events) and vicariance (four events) were important in shaping its current distribution. Although most species underwent stepwise colonization from East Asia via Kamchatka and Alaska to North America along the coast, a single lineage (Diaulota fulviventris and Diaulota harteri) crossed the Pacific Ocean directly from the north-western Pacific to the north-eastern Pacific, possibly via sea surface currents. [ABSTRACT FROM AUTHOR]

Simple Summary: The taxonomy of the sinica group of macaques has been unresolved due to inconsistencies between their physical traits and genetic relationships. To clarify this taxonomic issue, we analyzed DNA from previously unsampled populations of the macaques in the Himalayas. Our results revealed that the sinica group consists of seven distinct species, rather than the previously considered six species as the two subspecies of Assamese macaques (Macaca assamensis assamensis and M. a. pelops) are separate candidate species with strong genetic variations. The study also identified Arunachal macaques (M. munzala) in the Shannan area of Xizang Zizhiqu in China. Multiple analyses revealed complex historical patterns of species dispersal and separation, mostly linked to climatic changes during the Quaternary period. We propose a new hypothesis about the sinica group's evolutionary history. Owing to the taxonomic incongruence between the morphological features and genetic relationships of the sinica group of macaques (genus Macaca), the taxonomy of this macaque group has remained inconclusive. We aimed to resolve the taxonomic quandary and improve our understanding of the historical biogeography of the group by including macaque DNA samples from previously unsampled areas in the Himalayas. We sequenced and analyzed three mitochondrial DNA loci [cytochrome b (CYTB), cytochrome oxidase subunit 1 (COI) and D-loop; 2898 bp] for sequence polymorphism, phylogenetics, species delimitation, and ancestral area reconstruction. We confirmed the occurrence of Arunachal macaque (Macaca munzala) on the southern slopes of the Eastern Himalayas in the Xizang Zizhiqu (Tibet Autonomous Region) of China. The results revealed that the sinica group of macaques is a parapatric species group composed of seven distinct species. Phylogenetic and species delimitation analyses revealed that the two previously considered subspecies of Assamese macaques (the eastern subspecies M. assamensis assamensis and the western subspecies M. a. pelops) are two distinct species. The eastern Assamese macaque is a sister species to the Tibetan macaque, whereas the western Assamese macaque and Arunachal macaque are the closest genetic sister species. The sinica group of macaques underwent five vicariance and seven dispersal radiations in the past, which mainly coincided with the Quaternary climatic oscillations between the late Pliocene and the late Pleistocene. By integrating our phylogenetic and ancestral area reconstruction results with findings from previous paleontological and molecular studies, we propose a robust hypothesis about the phylogeography of the sinica group of macaques. [ABSTRACT FROM AUTHOR]

Two subspecies of the Yellow-throated Woodland Warbler Phylloscopus ruficapilla (family Phylloscopidae) have been recognised in South Africa based on the extent and intensity of yellow colouration. Our previous multi-locus population genetic survey across much of the Eastern Cape and southern KwaZulu-Natal provinces, conducted from 2017 to 2023, revealed a single homogenous regional population. That finding, derived from 93 individuals sampled from nine sites—six northeast of the Great Kei River (n = 72) and three to the southwest (n = 21)—did not support a subspecies boundary near the Great Kei River. Here, using 188 publicly archived photographic records for this species in South Africa, we show that the phenotypes of both subspecies are present on either side of this divide. The observed genetic homogeneity and lack of clear phenotypic vicariance suggest that P. ruficapilla is more dispersive than currently appreciated, and that the plumage-based subspecies may not represent significant population-level differences. [ABSTRACT FROM AUTHOR]

Narrow endemism is the core of plant diversity in flora of the Mediterranean Basin, which is among the world's 36 biodiversity hotspots. The Mediterranean genus Kundmannia (Careae, Apioideae) comprises just three species, K. sicula , K. anatolica , and K. syriaca. Notably, K. sicula has a wide distribution from the western Mediterranean to Greece, while K. anatolica and K. syriaca occur only in Turkey's Taurus Mountains, which is a phylogeographical hotspot. Initially, the aim herein was to determine the phylogenetic placement of the genus Kundmannia based on DNA sequences, but it later developed to describing a new genus, Antalia gen. nov. and revealing historical events that acted as drivers in the genetic divergence between Kundmannia and Antalia. Both ribosomal and combined chloroplast multilocus sequences were used to unravel the phylogenetic topology. Toward this aim, morphological characteristics were examined. Based on this, Antalia differs from Kundmannia by its shorter bracteoles and petals, the colour of the petals, and smaller fruits. The phylogenetic results revealed that the genus Kundmannia is nested within the tribe Careae and is not monophyletic. Antalia , which is genetically separate from Kundmannia , is described as a new genus. Detailed morphological descriptions and identification keys are provided. Causes of the genetic disjunction between Antalia and Kundmannia were carefully considered in a time-calibrated phylogenetic framework. The Mediterranean Sea has acted as a relatively effective barrier between these genera since the Messinian salinity crisis. The unwinged mericarps seem to have facilitated the work of the barrier. Historical events during and after the Pliocene and allopatric vicariance seem to have been the most important drivers of evolution between Kundmannia and Antalia and within Antalia. [ABSTRACT FROM AUTHOR]

Biogeographical reconstructions of the Indo-Australian Archipelago (IAA) have suggested a recent spread across the Sunda and Sahul shelves of lineages with diverse origins, which appears to be congruent with a geological history of recent tectonic uplift in the region. However, this scenario is challenged by new geological evidence suggesting that the Sunda shelf was never submerged prior to the Pliocene, casting doubt on the interpretation of recent uplift and the correspondence of evidence from biogeography and geology. A mismatch between geological and biogeographical data may occur if analyses ignore the dynamics of extinct lineages, because this may add uncertainty to the timing and origin of clades in biogeographical reconstructions. We revisit the historical biogeography of multiple IAA taxa and explicitly allow for the possibility of lineage extinction. In contrast to models assuming zero extinction, we find that all of these clades, including plants, invertebrates and vertebrates, have a common and widespread geographic origin, and each has spread and colonized the region much earlier than previously thought. The results for the eight clades re-examined in this article suggest that they diversified and spread during the early Eocene, which helps to unify the geological and biological histories of IAA. [ABSTRACT FROM AUTHOR]

Ever since Alfred Russel Wallace's nineteenth-century observation that related terrestrial species are often separated on opposing riverbanks, major Amazonian rivers have been recognized as key drivers of speciation. However, rivers are dynamic entities whose widths and courses may vary through time. It thus remains unknown how effective rivers are at reducing gene flow and promoting speciation over long timescales. We fit demographic models to genomic sequences to reconstruct the history of gene flow in three pairs of avian taxa fully separated by different Amazonian rivers, and whose geographic ranges do not make contact in headwater regions where rivers may cease to be barriers. Models with gene flow were best fit but still supported an initial period without any gene flow, which ranged from 187 000 to over 959 000 years, suggesting that rivers are capable of initiating speciation through long stretches of allopatric divergence. Allopatry was followed by either bursts or prolonged episodes of gene flow that retarded genomic differentiation but did not fully homogenize populations. Our results support Amazonian rivers as key barriers that promoted speciation and the build-up of species richness, but they also suggest that river barriers are often leaky, with genomic divergence accumulating slowly owing to episodes of substantial gene flow. [ABSTRACT FROM AUTHOR]

Gymnophthalmids are a diverse lineage of Neotropical lizards that present challenges in the understanding of their phylogenetic relationships and biogeographic history. Using a densely sampled phylogeny and distribution data, we investigated their biogeography at the family level. Dividing South and Central America into 12 regions, we tested six biogeographic models considering dispersal-extinction, vicariance, and founder events. Our analysis revealed high taxonomic and phylogenetic endemism in the Andes, Amazon, and Guiana Shield. The best-fit model identified the Guiana Shield as the likely ancestral area of the family, with dispersal events dominating over vicariance. Key areas for species interchange were the Amazon, Northern Andes, and Guiana Shield. The core regions of diversification included the Andes, Amazon, and Guiana Shield, with elevated species richness and biotic interchange events during the Eocene and Oligocene. The Guiana Shield stood out as a stronghold of gymnophthalmid diversity, driven by dispersal rates and ancient lineages. Our findings challenge previous hypotheses about the diversification of these lizards, suggesting a colonization pattern from lowlands to high elevations rather than the South-to-North Speciation Hypothesis for Andean lineages. [ABSTRACT FROM AUTHOR]

The marine gastropod genus Laevilitorina is exclusive to the Southern Hemisphere, with 21 species from southern South America, Antarctica, Australia, New Zealand, and sub-Antarctic Islands. We present a comprehensive revision of Laevilitorina , using molecular and morphological analyses, to address formally the interspecific divergences within the nominal taxon Laevilitorina caliginosa s.l. We confirm the validity of L. caliginosa and Laevilitorina venusta , and we demonstrate that specimens from the Strait of Magellan and Hornos Island constitute four new species here described: Laevilitorina magellanica sp. nov. Laevilitorina pepita sp. nov. Laevilitorina fueguina sp. nov. and Laevilitorina hicana sp. nov. All six species are clearly distinguishable genetically, morphologically, and through radular tooth shape and configurations. Laevilitorina venusta is broadly distributed across the Antarctic Peninsula, South Georgia, and sub-Antarctic Islands (Marion, Crozet, Kerguelen, and Macquarie), whereas L. caliginosa s.s. appears geographically restricted to Cape Horn, the Falkland/Malvinas Islands, and South Georgia. The identification of populations from Macquarie Island as L. caliginosa is dubious; we suggest that these records are likely to pertain to L. venusta. This detailed revision of Laevilitorina , whereby hidden diversity was detected, significantly enriches our knowledge of the evolutionary history of this group. [ABSTRACT FROM AUTHOR]

Recent taxonomic revision of the strikingly ornamented millipedes known as 'dragon millipedes' in the family Paradoxosomatidae, has revealed generic division into six genera. The majority of species are distributed in mainland South-East Asia and each genus is restricted to a well-delimited area. However, their evolutionary history has remained poorly understood, particularly the relationships among genera and their biogeographic distribution. We present a comprehensive and well-resolved molecular phylogeny based on mitochondrial and nuclear genes. A dataset of 256 sequences representing 40 dragon millipede species was newly generated and analysed in order to reveal the relationships and to explore the origin using ancestral range reconstruction. All dragon millipedes were retrieved together as monophyletic, each genus except Hylomus forming a distinct clade with strong statistical values, supporting the previous classification using morphology. A new monotypic genus and new species, Siamaxytes bifurca Srisonchai and Panha gen. nov. et sp. nov. was revealed based on distinct morphological and DNA data. The Tenasserim mountain range was inferred to be the centre of origin of dragon millipedes with a series of subsequent diversifications across mainland South-East Asia. Our analysis provides evidence that both dispersal and vicariance presumably played a role in shaping these millipedes' distribution and diversification. [ABSTRACT FROM AUTHOR]

Unraveling the phylogeographic histories of species remains a key endeavor for comprehending the evolutionary processes contributing to the rich biodiversity and high endemism found in East Asia. In this study, we explored the phylogeographic patterns and demographic histories of three endemic fishfly and dobsonfly species (Neochauliodes formosanus, Protohermes costalis, and Neoneuromus orientalis) belonging to the holometabolan order Megaloptera. These species, which share a broad and largely overlapping distribution, were analyzed using comprehensive mitogenomic data. Our findings revealed a consistent influence of vicariance on the population isolation of Neoc. formosanus and P. costalis between Hainan, Taiwan, and the East Asian mainland during the early Pleistocene, potentially hindering subsequent colonization of the later diverged Neon. orientalis to these islands. Additionally, we unveiled the dual function of the major mountain ranges in East Asia, serving both as barriers and conduits, in shaping the population structure of all three species. Notably, we demonstrated that these co-distributed species originated from Southwest, Southern, and eastern Central China, respectively, then subsequently migrated along multi-directional routes, leading to their sympatric distribution on the East Asian mainland. Furthermore, our results highlighted the significance of Pleistocene land bridges along the eastern coast of East Asia in facilitating the dispersal of mountain-dwelling insects with low dispersal ability. Overall, this study provides novel insight into the synergistic impact of Pleistocene geological and climatic events in shaping the diversity and distribution of aquatic insects in East Asia. [ABSTRACT FROM AUTHOR]

The geographic distribution and systematics of many groups of insects are still understudied across large geographic areas of the Iberian Peninsula. This lack of knowledge and the fact that many species have a complex evolutionary history due to the existence of "refugia within refugia" have hindered the taxonomic description of the true biodiversity in the Iberian Peninsula. Here, we discuss the evolutionary history of a flightless Iberian bush-cricket Antaxius spinibrachius (Fischer, 1853) using 1 nuclear and 2 mitochondrial markers. We applied species distribution modeling to design sampling strategies in climatically favorable areas and to detect missing isolated populations or unknown lineages. Following the species distribution modeled using all of the presence records available, we discovered 4 new isolated populations in Sierra Madrona, Serra de São Mamede, Sierra de Montánchez, and Sierra de la Demanda. Phylogenetic analyses recovered 2 major Pliocene lineages with a north–south geographic speciation pattern in the Iberian Peninsula. This north–south vicariant event split the common ancestor of these species on either side of the Tagus Valley, probably associated with the Pliocene climate change and the reorganization of paleobasins of the western Iberian Peninsula during the Miocene–Pliocene. We described the southern Iberian Plateau lineage of Antaxius as a new species of bush-cricket based on phylogenetic and morphological evidence, Antaxius oretanus sp. nov. We assessed the conservation status of the new species as "VU B2ab(iii,v)" under the IUCN criteria. [ABSTRACT FROM AUTHOR]

Delimitation of allopatric populations into species remains subjective and largely arbitrary. Many cold-adapted species from the sub-Arctic and Central and Southern European Mountain systems provide excellent models to study allopatry problem due to their patchy distributions. The same concerns many Holarctic species, which frequently show varying degrees of differentiation between continents. In this study, we analyze high-throughput target enrichment data for 10 groups of Arctic-alpine and Holarctic lepidopteran species sampled from different regions across the Holarctic realm, i.e. Fennoscandia, European Alps, Altai Mountains, and North America. We first aimed to assess whether the genetic differences in the nuclear genome reflected observed DNA barcode divergences and, secondly, whether the gap between population and species-level differences can be reliably dissected using genomic data. We compared the phylogenetic trees and uncorrected pairwise genetic distances obtained from target enrichment and mitochondrial COI barcodes and performed a suite of population genetic and species delimitation analyses to further explore patterns of intraspecific variation in our study species. We observed that in about one-half of the cases, DNA barcodes showed phylogenetic relationships similar to the target enrichment markers. Nuclear genetic differentiation varied among the populations analyzed, from low differentiation of geographically separated populations to the deeper separation of some Nearctic populations and Arctic-alpine disjunction in the populations from Fennoscandia and Southern European mountains. Our results highlight the need for consistent delimitation of allopatric populations, especially given the prevalence of distributional discontinuities across species. Large sets of standard genetic markers provide a very promising avenue towards this goal. [ABSTRACT FROM AUTHOR]

Several diatom species, including Cymbella amplificata, C. janischii and Navicula aurora, are largely restricted to Asia and western North America. These disjunctions likely represent recent long-distance dispersals or chance introductions. The two continents also support clusters of diatom species in several fossil and extant genera. One of these genera, Gomphosinica, is exclusive to the two continents but includes only one species in common. This suggests that these disjunct clusters of species arose from common precursors that underwent radiations while being separated for millennia. The divergence of these lineages likely began more than 25 Ma when island arcs of Asian (Siberian) origin docked on North America. The Asian/North American connection is not restricted to diatoms; vascular plants and dinosaur fossils also exhibit this connection. Differences between diatom floras east and west of the Rocky Mountains, as first noted by Ehrenberg, can be explained by differences in Earth history and geology. Researchers interested in diatom biogeography would do well to become familiar with the tectonic history and geology of their geographic regions of interest. Some cases of ‘invasive’ or ‘alien’ diatoms may simply be that changing conditions allowed existing but latent species to prosper and become apparent to the unaided eye. [ABSTRACT FROM AUTHOR]

The processes of forming lineages undergoing widespread radiations remain a knowledge gap that is fundamental to our understanding of the geographic distributions of species. Although early studies emphasized the importance of dispersal ability and historical migration events, key innovations that promote rapid diversification and/or adaptation to new habitats may also strongly influence distribution ranges. Juniperus is the second largest genus of conifers and is widely distributed throughout the Northern Hemisphere. Here, we used phylogenetic, phenotypic, and climatic data to investigate the contributions of these processes to the wide distribution and rapid diversification of Juniperus. Combining a time-scaled phylogeny and macroevolutionary theory, we show that the key innovations of berry-like seed cones and dioecy promoted the rapid diversification of Juniperus and that increased dispersal ability promoted allopatric speciation. Ecological niches had significant divergence among different clades of Juniperus. Biogeographic results supported multiple long-distance dispersal events and niche variation that contributed to the modern range of Juniperus, while both phenotypic adaptation and ecological opportunity probably drove its distribution range. Our findings suggest that the current widespread distribution is likely the result of significant divergence driven by niche variation in which ecological opportunities from key innovation and phenotypic divergence. Using the macroevolution method, this study shows that key innovations and niche divergence promoted widespread distribution and rapid diversification of Juniperus. [ABSTRACT FROM AUTHOR]

The separation of closely related terrestrial or freshwater species by vast marine barriers represents a biogeographical riddle. Such cases can provide evidence for vicariance, a process whereby ancient geological events like continental rifting divided ancestral geographical ranges. With an evolutionary history extending tens of millions of years, freshwater ecology, and distribution encompassing widely separated southern landmasses, osteoglossid bonytongue fishes are a textbook case of vicariance attributed to Mesozoic fragmentation of the Gondwanan supercontinent. Largely overlooked fossils complicate the clean narrative invoked for extant species by recording occurrences on additional continents and in marine settings. Here, we present a new total-evidence phylogenetic hypothesis for bonytongue fishes combined with quantitative models of range evolution and show that the last common ancestor of extant osteoglossids was likely marine, and that the group colonized freshwater settings at least four times when both extant and extinct lineages are considered. The correspondence between extant osteoglossid relationships and patterns of continental fragmentation therefore represents a striking example of biogeographical pseudocongruence. Contrary to arguments against vicariance hypotheses that rely only on temporal or phylogenetic evidence, these results provide direct palaeontological support for enhanced dispersal ability early in the history of a group with widely separated distributions in the modern day. [ABSTRACT FROM AUTHOR]

Theory links dispersal and diversity, predicting the highest diversity at intermediate dispersal levels. However, the modulation of this relationship by macro-eco-evolutionary mechanisms and competition within a landscape is still elusive. We examine the interplay between dispersal, competition and landscape structure in shaping biodiversity over 5 million years in a dynamic archipelago landscape. We model allopatric speciation, temperature niche, dispersal, competition, trait evolution and trade-offs between competitive and dispersal traits. Depending on dispersal abilities and their interaction with landscape structure, our archipelago exhibits two 'connectivity regimes', that foster speciation events among the same group of islands. Peaks of diversity (i.e. alpha, gamma and phylogenetic), occurred at intermediate dispersal; while competition shifted diversity peaks towards higher dispersal values for each connectivity regime. This shift demonstrates how competition can boost allopatric speciation events through the evolution of thermal specialists, ultimately limiting geographical ranges. Even in a simple landscape, multiple intermediate dispersal diversity relationships emerged, all shaped similarly and according to dispersal and competition strength. Our findings remain valid as dispersal- and competitive-related traits evolve and trade-off; potentially leaving identifiable biodiversity signatures, particularly when trade-offs are imposed. Overall, we scrutinize the convoluted relationships between dispersal, species interactions and landscape structure on macro-eco-evolutionary processes, with lasting imprints on biodiversity. This article is part of the theme issue 'Diversity-dependence of dispersal: interspecific interactions determine spatial dynamics'. [ABSTRACT FROM AUTHOR]

Species of the genus Eubranchus Forbes, 1838 (Mollusca: Gastropoda: Nudibranchia) are common faunistic elements of boreal benthic ecosystems, associated with hydroid communities. Recent studies have suggested that the widely distributed trans-Arctic E. rupium (Møller, 1842) constitutes a complex of at least three candidate species, but the detailed taxonomy of the complex remains unresolved. The purpose of the present paper is to conduct an integrative taxonomic study including molecular genetic methods (a phylogenetic analysis using COI , 16S rRNA and histone H3 with application of species delimitation methods) and morphological study (light and scanning electron microscopy) of E. rupium and closely related species. The specific aims of this study were to establish the species boundaries, morphological variability, and the phylogeographic structure within this group. The phylogeographic analysis included a TCS -based network analysis, an analysis of molecular variance (AMOVA), divergence time estimations, and ancestral area reconstructions. We demonstrate that specimens initially identified as E. rupium included three distinctive species: the nominal E. rupium with an amphiboreal range, the new species Eubranchus novik sp. nov. from the Sea of Japan, for which a taxonomic description is provided in this paper, and Eubranchus sp. from the northern Kuril Islands, which requires the collection and study of additional material for formal description. Our results confirm the amphiboreal distribution of E. rupium , as no geographic structure was found across Pacific, Arctic and Atlantic populations, and the results of the AMOVA analysis showed no differences between groups of samples from different geographic regions. The divergence of the ' Eubrancus rupium species complex' is estimated from the late Miocene or the Miocene–Pliocene boundary to the late Pliocene. It is hypothesised that the most probable ancestral region for the Eubranchus rupium species complex is the north-western Pacific, and the subsequent speciation likely occurred due to dispersal followed by allopatric speciation. ZooBank: Species of the genus Eubranchus Forbes, 1838 are common in boreal benthic ecosystems. Recent studies suggest the trans-Arctic Eubranchus rupium (Møller, 1842) is a species complex. This paper conducts an integrative taxonomic study of Eubranchus rupium and related species, confirming its amphiboreal distribution. The divergence of the species complex is estimated from the late Miocene or the Miocene–Pliocene boundary to the late Pliocene with the north-western Pacific as the probable ancestral region, followed by dispersal and allopatric speciation. (Image credit: Darya Grishina.) [ABSTRACT FROM AUTHOR]