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The recent advances in sequencing technologies, phylogenomics and divergence dating methods call for an integrative review of the current state of Hymenoptera systematics. We here explore the impact of these latest developments on the Hymenoptera phylogeny and our understanding of the timing of Hymenoptera evolution, while identifying the current methodological constraints and persistent knowledge gaps that warrant further investigation. Our review highlights the lack of consensus among the backbone phylogeny of Hymenoptera between key phylogenomic studies, as the higher level phylogeny remains unresolved in key nodes such as the relationships among Eusymphyta, the relationships within the Infraorder Proctotrupomorpha and the placements of the superfamilies Ichneumonoidea, Ceraphronoidea and Vespoidea. Furthermore, we underline the huge variation in divergence age estimates for Hymenoptera and detect several major gaps and/or disagreements between the fossil record and available age estimates, either due to the poorly studied fossil record or problematic age estimates, or both. To better understand the timing of Hymenoptera evolution and the role of key diversification factors, we will need continuous efforts to (i) reconcile conflicts among morphological and molecular phylogenies, by improving taxon sampling of underrepresented lineages, applying novel techniques to study morphology, making use of genome‐scale data and critically assessing incongruences in genetic markers; (ii) improve the Hymenoptera fossil record, by exercising integrative taxonomy and bringing together paleontologists and neontologists; and (iii) reconcile age estimates, by relying on tip dating approaches to bridge fossils, morphology and genomes across time. [ABSTRACT FROM AUTHOR]

The genus Stasimopus is endemic to South Africa but has never undergone a phylogeographic review. This study aims to unravel the phylogeographic patterns and history of the many Stasimopus species which occur in the greater Karoo region. A fossil‐calibrated phylogeny was produced based on three gene regions (CO1, 16S and EF‐1ɣ) for Stasimopus (Cor‐k‐lid trapdoor spiders) specimens collected in the Karoo region, to infer dates of origin and diversification. Demographic analyses were performed on species with sufficient sample sizes (> 4). Haplotype networks were constructed for each gene region and plotted on a map to infer phylogeographic patterns. Lastly, Mantel tests were performed to test for isolation by distance. It was found that 15 species occur in the Karoo and that the genus radiation in the area is in the early Palaeocene. Most diversification occurred between the late Eocene and the Miocene, coinciding with significant changes in climate. Several species show signals of demographic expansions. Isolation by distance was detected, but only with a slight correlation. It is apparent that aridification has played a vital role in the diversification of the genus in the Karoo region. This is a shared biogeographic influence between the mygalomorph fauna of the Karoo and arid region of western Australia. Stasimopus has radiated from the late Eocene and through the Miocene resulting in 15 extant species in the region. The Tankwa Karoo has been identified as a possible Pleistocene glacial cycle refugia for the species S. leipoldti. Many of the species in the Karoo are short‐range endemics, making them of high conservation concern. This study provided vital information as the Karoo is undergoing further desertification due to factors such as climate change, which may affect the future of short‐range endemic spiders. [ABSTRACT FROM AUTHOR]

Abstract Dormice (family Gliridae) are an ancient group of rodents. It was fully dominant in the Oligocene and Early Miocene, and its current diversity is represented by a few extant species. A Kazakhstani endemic, the desert dormouse Selevinia betpakdalaensis is one of the most enigmatic dormouse species. Lack of genetic data has not allowed Selevinia to be included in previous molecular phylogenetic analyses. In the current study, we report the first genetic data on S. betpakdalaensis as well as mitochondrial genomes of Myomimus roachi and Glirulus japonicus (retrieved from museum specimens) and a mitogenome of Graphiurus murinus (assembled from SRA data). The assembled mitochondrial genomes were combined with available mitochondrial data from GenBank to reconstruct the mitochondrial phylogeny of Gliridae. Taking into account a distortion of the phylogeny as a result of an analysis of the saturated third codon position, we obtained for the first time a resolved phylogeny of the family. The first split within Gliridae was estimated as an average of 34.6 Mya, whereas divergence time of subfamilies Graphiurinae and Glirinae was assessed at 32.67 Mya. The phylogenetic analysis confirmed the relationship (previously shown based on cranial and mandibular morphology) between Selevinia and the Myomimus.

The diversity of phytophagous insects is often attributed to the success of land plants in the framework of ecological speciation. Several hypotheses have been proposed to explain host plant driven insect diversification in a phylogenetic context and have mostly been explored using Lepidoptera. We posit that Miridae are a great system to examine these hypotheses because they are one of the largest primarily phytophagous insect families and include many species with narrow host repertoire. Focusing on the species‐rich Phylinae (>2700 spp.), we generate the most taxon‐rich phylogeny published to date and for the first time estimate divergence times and trace the evolution of host plant associations across the group. Focusing on two clades of oak‐associated phylines, we further examine if diversification in these insects and their hosts coincided or if the insects tracked their hosts. We find that Phylinae diverged from their orthotyline sister group before the end of the Cretaceous, tribal‐level taxa diversified throughout the Paleogene, and diversification within genera mostly occurred in the Neogene. Host plant repertoire reconstructions at the family level show transitions from stenophagy to polyphagy are more common than the reverse. We reconstructed the ancestral phyline host as ambiguous, followed by Asterales throughout most of the deep splits. Species‐level divergences in the two oak‐associated clades coincide with those in oaks, a pattern is that is consistent with the hypothesis that these plant bugs may have cospeciated with their hosts. Our study shows that Phylinae are a suitable system to further test hypotheses on ecological speciation of plants and insects but will require more robust phylogenetic hypotheses of the group. [ABSTRACT FROM AUTHOR]

Dormice (family Gliridae) are an ancient group of rodents. It was fully dominant in the Oligocene and Early Miocene, and its current diversity is represented by a few extant species. A Kazakhstani endemic, the desert dormouse Selevinia betpakdalaensis is one of the most enigmatic dormouse species. Lack of genetic data has not allowed Selevinia to be included in previous molecular phylogenetic analyses. In the current study, we report the first genetic data on S. betpakdalaensis as well as mitochondrial genomes of Myomimus roachi and Glirulus japonicus (retrieved from museum specimens) and a mitogenome of Graphiurus murinus (assembled from SRA data). The assembled mitochondrial genomes were combined with available mitochondrial data from GenBank to reconstruct the mitochondrial phylogeny of Gliridae. Taking into account a distortion of the phylogeny as a result of an analysis of the saturated third codon position, we obtained for the first time a resolved phylogeny of the family. The first split within Gliridae was estimated as an average of 34.6 Mya, whereas divergence time of subfamilies Graphiurinae and Glirinae was assessed at 32.67 Mya. The phylogenetic analysis confirmed the relationship (previously shown based on cranial and mandibular morphology) between Selevinia and the Myomimus. [ABSTRACT FROM AUTHOR]

This study explores how climate variables influenced the evolution and diversification of Neurergus newts within the Irano‐Anatolian biodiversity hotspot. We use a dated phylogenetic tree and climatic niche models to analyze their evolutionary history and ecological preferences. Using genetic data from nuclear (KIAA) and mitochondrial (16s and 12s) genes, we estimate divergence times and identify four major Neurergus clades. The initial speciation event occurred approximately 11.3 million years ago, coinciding with the uplift of the Zagros and Anatolian mountains. This geological transformation isolated newt populations, likely triggering the first speciation event. By integrating potential geographic distribution with climate variables, we reconstruct ancestral niche occupancy profiles. This highlights the critical roles of temperature and precipitation in shaping Neurergus habitat preferences and distribution. We observe both phylogenetic niche conservatism and divergence, with niche divergence playing a dominant role in diversification. This research emphasizes the complex interplay of geography, climate, and ecology in speciation and the vulnerability of isolated mountain newt populations to environmental changes. [ABSTRACT FROM AUTHOR]

ABSTRACT The genus Stasimopus is endemic to South Africa but has never undergone a phylogeographic review. This study aims to unravel the phylogeographic patterns and history of the many Stasimopus species which occur in the greater Karoo region. A fossil‐calibrated phylogeny was produced based on three gene regions (CO1, 16S and EF‐1ɣ) for Stasimopus (Cor‐k‐lid trapdoor spiders) specimens collected in the Karoo region, to infer dates of origin and diversification. Demographic analyses were performed on species with sufficient sample sizes (> 4). Haplotype networks were constructed for each gene region and plotted on a map to infer phylogeographic patterns. Lastly, Mantel tests were performed to test for isolation by distance. It was found that 15 species occur in the Karoo and that the genus radiation in the area is in the early Palaeocene. Most diversification occurred between the late Eocene and the Miocene, coinciding with significant changes in climate. Several species show signals of demographic expansions. Isolation by distance was detected, but only with a slight correlation. It is apparent that aridification has played a vital role in the diversification of the genus in the Karoo region. This is a shared biogeographic influence between the mygalomorph fauna of the Karoo and arid region of western Australia. Stasimopus has radiated from the late Eocene and through the Miocene resulting in 15 extant species in the region. The Tankwa Karoo has been identified as a possible Pleistocene glacial cycle refugia for the species S. leipoldti. Many of the species in the Karoo are short‐range endemics, making them of high conservation concern. This study provided vital information as the Karoo is undergoing further desertification due to factors such as climate change, which may affect the future of short‐range endemic spiders.

Abstract This study explores how climate variables influenced the evolution and diversification of Neurergus newts within the Irano‐Anatolian biodiversity hotspot. We use a dated phylogenetic tree and climatic niche models to analyze their evolutionary history and ecological preferences. Using genetic data from nuclear (KIAA) and mitochondrial (16s and 12s) genes, we estimate divergence times and identify four major Neurergus clades. The initial speciation event occurred approximately 11.3 million years ago, coinciding with the uplift of the Zagros and Anatolian mountains. This geological transformation isolated newt populations, likely triggering the first speciation event. By integrating potential geographic distribution with climate variables, we reconstruct ancestral niche occupancy profiles. This highlights the critical roles of temperature and precipitation in shaping Neurergus habitat preferences and distribution. We observe both phylogenetic niche conservatism and divergence, with niche divergence playing a dominant role in diversification. This research emphasizes the complex interplay of geography, climate, and ecology in speciation and the vulnerability of isolated mountain newt populations to environmental changes.

Simple Summary: Pygmy grasshoppers are a highly diverse group of insects that are distributed across China's landscapes. Their small size, limited flight capabilities, and reliance on humid habitats make them an intriguing subject to study evolution and biodiversity patterns. This research focused on improving the phylogenetic classification system of pygmy grasshoppers, which relies heavily on physical traits that can sometimes be misleading. We sequenced the complete mitochondrial DNA of four pygmy grasshopper species to reconstruct the evolutionary relationships among these species. Comparative analyses of new and existing DNA data revealed conflicts regarding the breadth of two generic groups—Systolederus and Tetrix. The Systolederus generic group encompasses too much diversity, necessitating taxonomic divisions, while Tetrix diversity appears restricted by overly splitting similar species. Further assessments uncovered over 150 million years of pygmy grasshopper ancestry and evidence for rapid habitat colonization abilities in the Tetrix generic group. By integrating genetic data, we refined perspectives on the evolutionary affinities of these insects. This approach demonstrates the importance of coupling morphological and molecular techniques for robust biodiversity assessments amidst the intricacies of adaptation and convergence. Resolving such taxonomic limitations will strengthen future initiatives to document and preserve pygmy grasshopper diversity across changing landscapes. Mitochondrial genomes offer pragmatic genetic markers to reconstruct evolutionary relationships and inform taxonomic classifications. Here, we present complete mitochondrial sequences for four Chinese pygmy grasshoppers (Tetrigidae), aiming to reevaluate phylogenetic patterns and morphological taxonomy. Our 17,643 bp, 16,274 bp, 15,086 bp, and 15,398 bp mitogenomes of Exothotettix guangxiensis, Formosatettix longwangshanensis, Euparatettix sinufemoralis and Systolederus zhengi, respectively, exhibit archetypal Tetrigidae architecture. We constructed phylogenies using 13 protein-coding loci from 39 Tetrigidae mitogenomes, revealing several genus-level clusters with statistically solid support, conflicts regarding Ex. guangxiensis, F. longwangshanensis merging into Tetrix, and two subclades of Systolederus. The dated divergence analysis indicates over 150 Mya of Tetrigidae ancestry, tracing the Systolederus generic group splits up to ~75 million years ago. Moreover, the Tetrix generic group radiated over 14 Mya across vast distributions, consistent with rapid adaptive dispersals. Our mitochondrial reconstructions suggest that Synstolederus is taxonomically overextended for a single genus, while the distinctiveness of Ex. guangxiensis and F. longwangshanensis from Tetrix appears questionable, and the Tetrix generic group comprises a potential tRNA-Ile coding region. Our integrative mitogenomic approaches will help resolve issues stemming from morphological taxonomy that is reliant on traits that are prone to convergence. This investigation enhances comprehension of Tetrigidae phylogeny and accentuates molecular systematics. [ABSTRACT FROM AUTHOR]

There is increasing evidence that demographic history and phylogeographic consequences of past climate changes unfolded locally and varied from region to region. Despite the high rodent species diversity and endemism in low latitude Asia, how they have responded to the past climatic fluctuations remains unexplored. In the present study, we trapped 253 murine individuals and sequenced their mitochondrial COI gene sequence. A total of ten species belonging to five genera were recognized through phylogenetic analyses. The results of divergence time estimation showed that the most common ancestors for all recognized species occurred in the Pleistocene. Signals of demographic expansion were detected in six species by at least one test and the events of sharp population size increase occurred asynchronously among species. The demographic expansion during the glaciation periods was corroborated by the expanded suitable distributional areas predicted by ecological niche modelling. The diversified demographic histories of rat communities in low-latitude Asia suggested that species might have responded to past regional environmental changes in an individualistic way. [ABSTRACT FROM AUTHOR]

Weevils have been shown to play significant roles in the obligate pollination of Australian cycads. In this study, we apply museomics to produce a first molecular phylogeny estimate of the Australian cycad weevils, allowing an assessment of their monophyly, placement and relationships. Divergence dating suggests that the Australian cycad weevils originated from the Late Oligocene to the Middle Miocene and that the main radiation of the cycad-pollinating groups occurred from the Middle to the Late Miocene, which is congruent with the diversification of the Australian cycads, thus refuting any notion of an ancient ciophilous system in Australia. Taxonomic studies reveal the existence of 19 Australian cycad weevil species and that their associations with their hosts are mostly non-species-specific. Co-speciation analysis shows no extensive co-speciation events having occurred in the ciophilous system of Australian cycads. The distribution pattern suggests that geographical factors, rather than diversifying coevolution, constitute the overriding process shaping the Australian cycad weevil diversity. The synchronous radiation of cycads and weevil pollinators is suggested to be a result of the post-Oligocene diversification common in Australian organisms. [ABSTRACT FROM AUTHOR]

Mitochondrial genomes offer pragmatic genetic markers to reconstruct evolutionary relationships and inform taxonomic classifications. Here, we present complete mitochondrial sequences for four Chinese pygmy grasshoppers (Tetrigidae), aiming to reevaluate phylogenetic patterns and morphological taxonomy. Our 17,643 bp, 16,274 bp, 15,086 bp, and 15,398 bp mitogenomes of Exothotettix guangxiensis, Formosatettix longwangshanensis, Euparatettix sinufemoralis and Systolederus zhengi, respectively, exhibit archetypal Tetrigidae architecture. We constructed phylogenies using 13 protein-coding loci from 39 Tetrigidae mitogenomes, revealing several genus-level clusters with statistically solid support, conflicts regarding Ex. guangxiensis, F. longwangshanensis merging into Tetrix, and two subclades of Systolederus. The dated divergence analysis indicates over 150 Mya of Tetrigidae ancestry, tracing the Systolederus generic group splits up to ~75 million years ago. Moreover, the Tetrix generic group radiated over 14 Mya across vast distributions, consistent with rapid adaptive dispersals. Our mitochondrial reconstructions suggest that Synstolederus is taxonomically overextended for a single genus, while the distinctiveness of Ex. guangxiensis and F. longwangshanensis from Tetrix appears questionable, and the Tetrix generic group comprises a potential tRNA-Ile coding region. Our integrative mitogenomic approaches will help resolve issues stemming from morphological taxonomy that is reliant on traits that are prone to convergence. This investigation enhances comprehension of Tetrigidae phylogeny and accentuates molecular systematics.

In this paper, we report the complete mitochondrial genome of the northern smooth-tailed treeshrew Dendrogale murina, which was sequenced for the first time using the Illumina next-generation sequencing (NGS) technology. The total length of the mitochondrial genome is 16,844–16,850 bp and encodes 37 genes, including two ribosomal RNAs (rRNAs) 12S and 16S, 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), and a D-loop in the characteristic arrangement of family Tupaiidae (Mammalia: Scandentia). The overall base composition of the complete mitochondrial DNA is A (33.5%), C (25.5%), G (13.9%), and T (27.1%). Phylogenetic analysis of Scandentia mitochondrial genomes showed a classic pattern, which was revealed previously while using individual phylogenetic markers. The result of the current study is consistent with one based on the latest morphological studies, with the basal position of Ptilocercus and Dendrogale sister to the rest of the Tupaiidae genera. The divergence time of the Dendrogale genus is estimated as Eocene–Oligocene, with the mean value of 35.8 MYA, and the Ptilocercus genus probably separated at about 46.3 MYA. We observe an increase in the age of all nodes within the Scandentia, except for a decrease in the age of separation of Ptilocercus. This result can be explained both by the addition of new mitochondrial genome data in the analysis and the usage of new calibration points from recently published data. [ABSTRACT FROM AUTHOR]

Recent time-calibrated amphibian phylogenies agree on the family-level relationships among extant salamanders but had disparate sampling regimes and inferred very different divergence times. For example, a recent phylogenomic study based on 220 nuclear loci had limited taxon sampling (41 species) and estimated relatively young divergence dates, whereas a more extensive supermatrix study based on 15 genes and 481 species estimated dates that were 22-45 million years older for major clades. Here, we combined phylogenomic and supermatrix approaches to estimate the largest salamander phylogeny to date based on molecular markers. Our matrix contained 765 salamander species and 503 genes (with 92.3% missing data overall). We included 284 more species than the previous largest salamander phylogeny (59% increase) and sampled approximately 93% of all currently described salamander species. Our dating analyses incorporated more than twice as many fossil calibration points within salamanders as previous studies. Maximum-likelihood estimates of tree topology yielded family-level relationships that were consistent with earlier studies. Nearly all species were placed in the expected genera, despite extensive missing data in many species. Bootstrap support was generally high across the tree but was poor in some clades where sampling of genes was limited (e.g., among some bolitoglossine salamanders). The dating analyses yielded age estimates for major clades that were generally intermediate between those from the previous phylogenomic and supermatrix analyses. We also provide a set of 200 time-calibrated trees for use in comparative analyses., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

The greater kudu (Tragelaphus strepsiceros) is widespread throughout South Africa and occurs in higher densities in the north-eastern regions, with isolated populations in the Eastern Cape Province and in the Kimberley area in the Northern Cape Province. This study aimed to assess the phylogeographic structure of regional South African greater kudu groups, based on neutral mitochondrial DNA regions as well as adaptive variation. A total of 116 kudu were sampled from across the South African distribution range, separated by geographic features and distance, from six South African provinces. Sampling was mainly based on skin samples collected from taxidermists. Genetic diversity and differentiation were quantified using sequence data from the mitochondrial control region (mtDNA CR) and the heat shock protein subunit 5 (HSPA5) gene. Short tandem repeat (STR) sequences were identified at the 3′-UTR of the bone morphogenetic protein 4 (BMP4) gene and used for downstream analyses. Twenty-six haplotypes were identified from the CR dataset, three for the HSPA5 region, and 14 alleles were identified for the BMP4 STR. The CR phylogenetic analyses identified two distinct genetic clades representing an Eastern and Western group respectively. Molecular divergence dating identified the most recent common ancestor of the Eastern and Western South African kudu clades as older (2.237 Mya) than some well-known African antelope species. This result was consistent with the HSPA5 and BMP4 results. Environmental selective pressures, such as rainfall and ambient temperature, were also identified as possible driving forces for evolution at the HSPA5 gene region. Overall, these results can provide support for future management decisions to ensure the conservation of natural patterns of diversity in this majestic antelope species in South Africa. [ABSTRACT FROM AUTHOR]

Abstract Multiple geological and climatic events have created geographical or ecological barriers associated with speciation events, playing a role in biological diversification in North and Central America. Here, we evaluate the influence of the Neogene and Quaternary geological events, as well as the climatic changes in the diversification of the colubrid snake genus Rhadinaea using molecular dating and ancestral area reconstruction. A multilocus sequence dataset was generated for 37 individuals of Rhadinaea from most of the biogeographical provinces where the genus is distributed, representing 19 of the 21 currently recognized species, and two undescribed species. Our analyses show that the majority of the Rhadinaea species nest in two main clades, herein identified as “Eastern” and “Southern”. These clades probably diverged from each other in the early Miocene, and their divergence was followed by 11 divergences during the middle to late Miocene, three divergences during the Pliocene, and six divergences in the Pleistocene. The ancestral distribution of Rhadinaea was reconstructed across the Sierra Madre del Sur. Our phylogenetic analyses do not support the monophyly of Rhadinaea. The Miocene and Pliocene geomorphology, perhaps in conjunction with climate change, appears to have triggered the diversification of the genus, while the climatic changes during the Miocene probably induced the diversification of Rhadinaea in the Sierra Madre del Sur. Our analysis suggests that the uplifting of the Trans‐Mexican Volcanic Belt and Chiapan–Guatemalan highlands in this same period resulted in northward and southward colonization events. This was followed by more recent, independent colonization events in the Pliocene and Pleistocene involving the Balsas Basin, Chihuahuan Desert, Pacific Coast, Sierra Madre Occidental, Sierra Madre Oriental, Sierra Madre del Sur, Trans‐Mexican Volcanic Belt, and Veracruz provinces, probably driven by the climatic fluctuations of the time.

Abstract Background The orogeny of the eastern Mediterranean region has substantially affected ecological speciation patterns, particularly of mountain-dwelling species. Mountain vipers of the genus Montivipera are among the paramount examples of Mediterranean neo-endemism, with restricted ranges in the mountains of Anatolia, the Levant, Caucasus, Alborz, and Zagros. Here we explore the phylogenetic and ecological diversification of Montivipera to reconstruct its ecological niche evolution and biogeographic history. Using 177 sequences of three mitochondrial genes, a dated molecular phylogeny of mountain vipers was reconstructed. Based on 320 occurrence points within the entire range of the genus and six climatic variables, ecological niches were modelled and used to infer ancestral niche occupancy. In addition, the biogeographic history and ancestral states of the species were reconstructed across climate gradients. Results Dated phylogenetic reconstruction revealed that the ancestor of mountain vipers split into two major clades at around 12.18 Mya followed by multiple vicariance events due to rapid orogeny. Montivipera colonised coastal regions from a mountain-dwelling ancestor. We detected a highly complex ecological niche evolution of mountain vipers to temperature seasonality, a variable that also showed a strong phylogenetic signal and high contribution in niche occupation. Conclusion Raising mountain belts in the Eastern Mediterranean region and subsequent remarkable changes in temperature seasonality have led to the formation of important centres of diversification and endemism in this biodiversity hotspot. High rates of niche conservatism, low genetic diversity, and segregation of ranges into the endemic distribution negatively influenced the adaptive capacity of mountain vipers. We suggest that these species should be considered as evolutionary significant units and priority species for conservation in Mediterranean mountain ecosystems.

Abstract The structure and sequence of plastid genomes is highly conserved across most land plants, except for a minority of lineages that show gene loss and genome degradation. Understanding the early stages of plastome degradation may provide crucial insights into the repeatability and predictability of genomic evolutionary trends. We investigated these trends in subtribe Gentianinae of the Gentianaceae, which encompasses ca. 450 species distributed around the world, particularly in alpine and subalpine environments. We sequenced, assembled, and annotated the plastomes of 41 species, representing all six genera in subtribe Gentianinae and all main sections of the species‐rich genus Gentiana L. We reconstructed the phylogeny, estimated divergence times, investigated the phylogenetic distribution of putative gene losses, and related these to substitution rate shifts and species’ habitats. We obtained a strongly supported topology consistent with earlier studies, with all six genera in Gentianinae recovered as monophyletic and all main sections of Gentiana having full support. While closely related species have very similar plastomes in terms of size and structure, independent gene losses, particularly of the ndh complex, have occurred in multiple clades across the phylogeny. Gene loss was usually associated with a shift in the boundaries of the small single‐copy and inverted repeat regions. Substitution rates were variable between clades, with evidence for both elevated and decelerated rate shifts. Independent lineage‐specific loss of ndh genes occurred at a wide range of times, from Eocene to Pliocene. Our study illustrates that diverse degradation patterns shape the evolution of the plastid in this species‐rich plant group.

Multiple geological and climatic events have created geographical or ecological barriers associated with speciation events, playing a role in biological diversification in North and Central America. Here, we evaluate the influence of the Neogene and Quaternary geological events, as well as the climatic changes in the diversification of the colubrid snake genus Rhadinaea using molecular dating and ancestral area reconstruction. A multilocus sequence dataset was generated for 37 individuals of Rhadinaea from most of the biogeographical provinces where the genus is distributed, representing 19 of the 21 currently recognized species, and two undescribed species. Our analyses show that the majority of the Rhadinaea species nest in two main clades, herein identified as "Eastern" and "Southern". These clades probably diverged from each other in the early Miocene, and their divergence was followed by 11 divergences during the middle to late Miocene, three divergences during the Pliocene, and six divergences in the Pleistocene. The ancestral distribution of Rhadinaea was reconstructed across the Sierra Madre del Sur. Our phylogenetic analyses do not support the monophyly of Rhadinaea. The Miocene and Pliocene geomorphology, perhaps in conjunction with climate change, appears to have triggered the diversification of the genus, while the climatic changes during the Miocene probably induced the diversification of Rhadinaea in the Sierra Madre del Sur. Our analysis suggests that the uplifting of the Trans‐Mexican Volcanic Belt and Chiapan–Guatemalan highlands in this same period resulted in northward and southward colonization events. This was followed by more recent, independent colonization events in the Pliocene and Pleistocene involving the Balsas Basin, Chihuahuan Desert, Pacific Coast, Sierra Madre Occidental, Sierra Madre Oriental, Sierra Madre del Sur, Trans‐Mexican Volcanic Belt, and Veracruz provinces, probably driven by the climatic fluctuations of the time. [ABSTRACT FROM AUTHOR]

[Display omitted] • The >250 species of Delias live throughout Asia, Australia, and Melanesia. • Frequent inter-island dispersal during the Neogene triggered diversification. • Lineages on New Guinea began diversifying ca. 5 Mya as the island's central highlands were forming. • We use our large taxon sample to categorize all described species into species groups. The world's largest butterfly genus Delias , commonly known as Jezebels, comprises ca. 251 species found throughout Asia, Australia, and Melanesia. Most species are endemic to islands in the Indo-Australian Archipelago or to New Guinea and nearby islands in Melanesia, and many species are restricted to montane habitats over 1200 m. We inferred an extensively sampled and well-supported molecular phylogeny of the group to better understand the spatial and temporal dimensions of its diversification. The remarkable diversity of Delias evolved in just ca. 15–16 Myr (crown age). The most recent common ancestor of a clade with most of the species dispersed out of New Guinea ca. 14 Mya, but at least six subsequently diverging lineages dispersed back to the island. Diversification was associated with frequent dispersal of lineages among the islands of the Indo-Australian Archipelago, and the divergence of sister taxa on a single landmass was rare and occurred only on the largest islands, most notably on New Guinea. We conclude that frequent inter-island dispersal during the Neogene—likely facilitated by frequent sea level change—sparked much diversification during that period. Many extant New Guinea lineages started diversifying 5 Mya, suggesting that orogeny facilitated their diversification. Our results largely agree with the most recently proposed species group classification system, and we use our large taxon sample to extend this system to all described species. Finally, we summarize recent insights to speculate how wing pattern evolution, mimicry, and sexual selection might also contribute to these butterflies' rapid speciation and diversification. [ABSTRACT FROM AUTHOR]

Abstract Background Xanthomonas citri subsp. citri pathotypes cause bacterial citrus canker, being responsible for severe agricultural losses worldwide. The A pathotype has a broad host spectrum, while A* and Aw are more restricted both in hosts and in geography. Two previous phylogenomic studies led to contrasting well-supported clades for sequenced genomes of these pathotypes. No extensive biogeographical or divergence dating analytic approaches have been so far applied to available genomes. Results Based on a larger sampling of genomes than in previous studies (including six new genomes sequenced by our group, adding to a total of 95 genomes), phylogenomic analyses resulted in different resolutions, though overall indicating that A + AW is the most likely true clade. Our results suggest the high degree of recombination at some branches and the fast diversification of lineages are probable causes for this phylogenetic blurring effect. One of the genomes analyzed, X. campestris pv. durantae, was shown to be an A* strain; this strain has been reported to infect a plant of the family Verbenaceae, though there are no reports of any X. citri subsp. citri pathotypes infecting any plant outside the Citrus genus. Host reconstruction indicated the pathotype ancestor likely had plant hosts in the family Fabaceae, implying an ancient jump to the current Rutaceae hosts. Extensive dating analyses indicated that the origin of X. citri subsp. citri occurred more recently than the main phylogenetic splits of Citrus plants, suggesting dispersion rather than host-directed vicariance as the main driver of geographic expansion. An analysis of 120 pathogenic-related genes revealed pathotype-associated patterns of presence/absence. Conclusions Our results provide novel insights into the evolutionary history of X. citri subsp. citri as well as a sound phylogenetic foundation for future evolutionary and genomic studies of its pathotypes.

Background: The orogeny of the eastern Mediterranean region has substantially affected ecological speciation patterns, particularly of mountain-dwelling species. Mountain vipers of the genus Montivipera are among the paramount examples of Mediterranean neo-endemism, with restricted ranges in the mountains of Anatolia, the Levant, Caucasus, Alborz, and Zagros. Here we explore the phylogenetic and ecological diversification of Montivipera to reconstruct its ecological niche evolution and biogeographic history. Using 177 sequences of three mitochondrial genes, a dated molecular phylogeny of mountain vipers was reconstructed. Based on 320 occurrence points within the entire range of the genus and six climatic variables, ecological niches were modelled and used to infer ancestral niche occupancy. In addition, the biogeographic history and ancestral states of the species were reconstructed across climate gradients. Results: Dated phylogenetic reconstruction revealed that the ancestor of mountain vipers split into two major clades at around 12.18 Mya followed by multiple vicariance events due to rapid orogeny. Montivipera colonised coastal regions from a mountain-dwelling ancestor. We detected a highly complex ecological niche evolution of mountain vipers to temperature seasonality, a variable that also showed a strong phylogenetic signal and high contribution in niche occupation. Conclusion: Raising mountain belts in the Eastern Mediterranean region and subsequent remarkable changes in temperature seasonality have led to the formation of important centres of diversification and endemism in this biodiversity hotspot. High rates of niche conservatism, low genetic diversity, and segregation of ranges into the endemic distribution negatively influenced the adaptive capacity of mountain vipers. We suggest that these species should be considered as evolutionary significant units and priority species for conservation in Mediterranean mountain ecosystems. [ABSTRACT FROM AUTHOR]

The tropics contain many of the most biodiverse regions on Earth but the processes responsible for generating this diversity remain poorly understood. This study investigated the drivers of diversification in arthropods with stenotopic ecological requirements and limited dispersal capability using as a model the monotypic whip spider (Amblypygi) genus Acanthophrynus, widespread in the tropical deciduous forests of Mexico. We hypothesized that for these organisms, the tropical deciduous forests serve as a conduit for dispersal, with their disappearance imposing barriers. Given that these forests are located in a region of complex geological history and that they fluctuated in extent during the Pliocene–Pleistocene glacial/interglacial cycles we combine molecular divergence dating, palaeoclimatic niche modelling and ancestral area reconstruction to test if and when habitat fragmentation promoted diversification in Acanthophrynus. Concomitant with the expected role of landscape change, we demonstrate that orogeny of the Trans‐Mexican Volcanic Belt, in the Late Miocene or Early Pliocene (6.95–5.21 million years ago), drove the earliest divergence of Acanthophrynus by vicariance. Similarly, as expected, the later onset of glaciations strongly impacted diversification. Whereas a more stable climate in the southern part of the distribution enabled further diversification, a marked loss of suitable habitat during the glaciations only allowed dispersal and diversification in the north to occur later, resulting in a lower overall diversity in this region. Barriers and diversification patterns identified in Acanthophrynus are reflected in the phylogeography of codistributed vertebrates and arthropods, emphasizing the profound impact of Trans‐Mexican Volcanic Belt orogeny and glacial/interglacial cycles as drivers of diversification in the Mexican Neotropics. [ABSTRACT FROM AUTHOR]

Several recent studies have suggested past gene flow between the Przewalski's horse and modern domestic horse and questioned the wild origin of the Przewalski's horse. Mitochondrial DNA has placed representatives of the Przewalski's horse into three among the eighteen haplogroups detected from the modern horse. Of these, two haplogroups have so far been found exclusively in the Przewalski's horse, while the one shared with the domestic horse includes captive individuals that have uncertain pedigrees. We recently found five domestic horse individuals of North European horse breeds to carry a mitochondrial haplogroup that was previously confined only to the Przewalski's horse. These individuals were sequenced for 6039 bp of mitochondrial DNA and used, together with domestic and Przewalski's horse sequences presenting all horse haplogroups, to examine the phylogenetic relationships and to date the divergence time between Przewalski's and domestic horse clusters within this haplogroup. The divergence was dated to have likely occurred about 13,300–11,400 years ago, which coincides with the time of the Younger Dryas. [ABSTRACT FROM AUTHOR]

The structure and sequence of plastid genomes is highly conserved across most land plants, except for a minority of lineages that show gene loss and genome degradation. Understanding the early stages of plastome degradation may provide crucial insights into the repeatability and predictability of genomic evolutionary trends. We investigated these trends in subtribe Gentianinae of the Gentianaceae, which encompasses ca. 450 species distributed around the world, particularly in alpine and subalpine environments. We sequenced, assembled, and annotated the plastomes of 41 species, representing all six genera in subtribe Gentianinae and all main sections of the species‐rich genus Gentiana L. We reconstructed the phylogeny, estimated divergence times, investigated the phylogenetic distribution of putative gene losses, and related these to substitution rate shifts and species' habitats. We obtained a strongly supported topology consistent with earlier studies, with all six genera in Gentianinae recovered as monophyletic and all main sections of Gentiana having full support. While closely related species have very similar plastomes in terms of size and structure, independent gene losses, particularly of the ndh complex, have occurred in multiple clades across the phylogeny. Gene loss was usually associated with a shift in the boundaries of the small single‐copy and inverted repeat regions. Substitution rates were variable between clades, with evidence for both elevated and decelerated rate shifts. Independent lineage‐specific loss of ndh genes occurred at a wide range of times, from Eocene to Pliocene. Our study illustrates that diverse degradation patterns shape the evolution of the plastid in this species‐rich plant group. [ABSTRACT FROM AUTHOR]

The Lycini (Elateroidea: Lycidae) contains > 400 species placed in four typologically based genera and numerous subgenera. We assembled a mito-ribosomal dataset representing ~100 species from the whole range and recovered a phylogeny rejecting Lycus and Lycostomus as polyphyletic assemblages. The male-specific wide elytra and elytral thorns are identified in unrelated Neolycus and Lycus. The morphological similarity based on sexual dimorphism and aposematic patterns defined terminal clades and misled the genus-rank classification. We delimit Neolycus , Rhyncheros reinst. name (= Thoracocalon syn. nov. = Lyconotus syn. nov.), Lipernes Lycostomus , Haplolycus and Lycus. Demosis and six subgenera of Lycus are synonymized with Lycus. Celiasis Laporte, 1840 is kept in the classification as a nomen dubium until any specimen is available. The deep lineages are known from the Americas and Asia. Africa was colonized by Lycus and Haplolycus. Each specific aposematic pattern occurs in a limited range, and the similar body shape and coloration evolved in unrelated sympatrically occurring lineages. High intraspecific polymorphism is putatively a result of the adaptation of various populations to local mimetic assemblages. Therefore, the delimitation of many phenotypically diverse species should be investigated. [ABSTRACT FROM AUTHOR]

Abstract Background Plukenetia is a small pantropical genus of lianas and vines with variably sized edible oil-rich seeds that presents an ideal system to investigate neotropical and pantropical diversification patterns and seed size evolution. We assessed the biogeography and seed evolution of Plukenetia through phylogenetic analyses of a 5069 character molecular dataset comprising five nuclear and two plastid markers for 86 terminals in subtribe Plukenetiinae (representing 20 of ~ 23 Plukenetia species). Two nuclear genes, KEA1 and TEB, were used for phylogenetic reconstruction for the first time. Our goals were: (1) produce a robust, time-dependent evolutionary framework for Plukenetia using BEAST; (2) reconstruct its biogeographical history with ancestral range estimation in BioGeoBEARS; (3) define seed size categories; (4) identify patterns of seed size evolution using ancestral state estimation; and (5) conduct regression analyses with putative drivers of seed size using the threshold model. Results Plukenetia was resolved into two major groups, which we refer to as the pinnately- and palmately-veined clades. Our analyses suggest Plukenetia originated in the Amazon or Atlantic Forest of Brazil during the Oligocene (28.7 Mya) and migrated/dispersed between those regions and Central America/Mexico throughout the Miocene. Trans-oceanic dispersals explain the pantropical distribution of Plukenetia, including from the Amazon to Africa in the Early Miocene (17.4 Mya), followed by Africa to Madagascar and Africa to Southeast Asia in the Late Miocene (9.4 Mya) and Pliocene (4.5 Mya), respectively. We infer a single origin of large seeds in the ancestor of Plukenetia. Seed size fits a Brownian motion model of trait evolution and is moderately to strongly associated with plant size, fruit type/dispersal syndrome, and seedling ecology. Biome shifts were not drivers of seed size, although there was a weak association with a transition to fire prone semi-arid savannas. Conclusions The major relationships among the species of Plukenetia are now well-resolved. Our biogeographical analyses support growing evidence that many pantropical distributions developed by periodic trans-oceanic dispersals throughout the Miocene and Pliocene. Selection on a combination of traits contributed to seed size variation, while movement between forest edge/light gap and canopy niches likely contributed to the seed size extremes in Plukenetia.

Whiteflies (Hemiptera: Sternorrhyncha: Aleyrodidae) are a superfamily of small phloem-feeding insects. They rely on their primary endosymbionts " Candidatus Portiera aleyrodidarum" to produce essential amino acids not present in their diet. Portiera has been codiverging with whiteflies since their origin and therefore reflects its host's evolutionary history. Like in most primary endosymbionts, the genome of Portiera stays stable across the Aleyrodidae superfamily after millions of years of codivergence. However, Portiera of the whitefly Bemisia tabaci has lost the ancestral genome order, reflecting a rare event in the endosymbiont evolution: the appearance of genome instability. To gain a better understanding of Portiera genome evolution, identify the time point in which genome instability appeared and contribute to the reconstruction of whitefly phylogeny, we developed a new phylogenetic framework. It targeted five Portiera genes and determined the presence of the DNA polymerase proofreading subunit (dnaQ) gene, previously associated with genome instability, and two alternative gene rearrangements. Our results indicated that Portiera gene sequences provide a robust tool for studying intergenera phylogenetic relationships in whiteflies. Using these new framework, we found that whitefly species from the Singhiella , Aleurolobus , and Bemisia genera form a monophyletic tribe, the Aleurolobini, and that their Portiera exhibit genome instability. This instability likely arose once in the common ancestor of the Aleurolobini tribe (at least 70 Ma), drawing a link between the appearance of genome instability in Portiera and the switch from multibacteriocyte to a single-bacteriocyte mode of inheritance in this tribe. [ABSTRACT FROM AUTHOR]

Although Conraua goliath is well known as the largest living frog species, the diversity and evolution of the genus Conraua across sub‐Saharan Africa remain poorly understood. We present multilocus phylogenetic analyses of the six currently recognized species that provide insights into divergence times, biogeography, body size evolution and undescribed species. An analysis of divergence times demonstrates that crown‐group Conraua arose some time during the latest Oligocene to mid‐Miocene followed by divergence into major lineages in the mid‐Miocene that may reflect the fragmentation of widespread tropical forests in Africa that began at this time. We find three pairs of sister species, C. crassipes + C. beccarii, C. alleni + C. derooi and C. goliath + C. robusta, each of which diverged during the Miocene. These relationships reject phylogenetic hypotheses based solely on biogeography as the geographically peripheral C. beccarii from north‐eastern Africa is nested within western African species and the Central African species do not form a clade. Our species delimitation analyses provide support for undescribed species in C. alleni, C. beccarii and C. derooi, and possibly C. crassipes, suggesting that the current taxonomy substantially underestimates species diversity. There is no clear directional trend of either increasing or decreasing body size in Conraua and the three largest species do not form a clade. With a robust phylogenetic hypothesis in hand, further field‐based studies are needed to understand the evolution of morphology and life history in this charismatic African anuran clade. [ABSTRACT FROM AUTHOR]

Abstract Background Recent studies have begun to reveal the complex evolutionary and biogeographic histories of mainland anoles in Central America, but the origins and relationships of many taxa remain poorly understood. One such group is the Anolis (Norops) crassulus species subgroup, which contains ten morphologically similar highland taxa, the majority of which have restricted distributions. The nominal taxon A. crassulus has a disjunct distribution from Chiapas, Mexico, through Guatemala, in the highlands of El Salvador, and in the Chortís Highlands of Honduras. We test the relationships of these species using multiple mitochondrial and nuclear loci in concatenated and multispecies coalescent frameworks, in an effort to both resolve long-standing taxonomic confusion and present new insights into the evolution and biogeography of these taxa. Results Sequences of multiple mitochondrial and nuclear loci were generated for eight of the ten species of the Anolis crassulus species subgroup. We analyzed phylogenetic relationships and estimated divergence times and ancestral ranges of the subgroup, recovering a monophyletic subgroup within Anolis. Within the nominal taxon Anolis crassulus, we recovered multiple genetically distinct lineages corresponding to allopatric populations, and show that the Chortís Highland lineage split from the others over 13 MYA. Additionally, distinct mitochondrial lineages are present within the taxa A. heteropholidotus and A. morazani, and importantly, samples of A. crassulus and A. sminthus previously used in major anole phylogenetic analyses are not recovered as conspecific with those taxa. We infer a Chortís Highland origin for the ancestor of this subgroup, and estimate cladogenesis of this subgroup began approximately 22 MYA. Conclusions Our results provide new insights into the evolution, biogeography, and timing of diversification of the Anolis crassulus species subgroup. The disjunctly distributed Anolis crassulus sensu lato represents several morphologically conserved, molecularly distinct anoles, and several other species in the subgroup contain multiple isolated lineages.

The water toad (Bufo stejnegeri) is endemic to Northeastern Asia (South Korea, North Korea, and China) and has unique ecology for a toad by being semi-aquatic and breeding in lotic environments. We use a suite of phylogenetic analyses to understand the evolution of B. stejnegeri's distinctive ecology and the impact of Pleistocene glacial cycles on the biodiversity of Northeast Asia. For the evolution of a semi-aquatic lifestyle, although B. stejnegeri is relatively closely related to two other semi-aquatic Bufo species (B. torrenticola and B. andrewsi), ancestral state reconstruction analysis infers an independent evolution in all three species. Upon closer inspection, B. stejnegeri exhibits major differences in amplexus and egg-laying behavior compared to the other two species, supporting independent evolution. Divergence dating analyses infer B. stejnegeri to have originated during the Late Miocene-Early Pliocene (4.3 Ma, 2.7–6.2 Ma). This species does not exhibit population differentiation with respect to mountain range, but shows a preliminary genetic pattern of southern richness and northern purity supporting a single refugium in Korea during Pleistocene glacial cycles. The Bayesian skyline plot supports this inference, suggesting a population decline followed by expansion during the Pleistocene. Although not as species rich as the tropics, we hope this study helps spark interest in Northeast Asian biodiversity.

Sky Islands are high-elevation environments that are separated by warmer, low elevations, forming natural patches of unique montane habitat that often persist through changing climates. Peninsular India was ancestrally forested and has gradually become more arid since at least the Oligocene, and open landscapes have dominated since the middle-late Miocene. Mesic forests today are largely restricted to coastal mountains and some other montane habitats. A mitochondrial phylogeny and fossil-calibrated timetree of Indian Hemiphyllodactylus reveal an Indochinese origin and an endemic radiation with 12 species-level lineages, where a single species was known, that diversified in the Oligocene-Miocene across montane forest habitats in the Eastern Ghats and south India. The phylogeny also suggests the discontinuous Eastern Ghats mountain range encompasses two distinct biogeographic entities: north and south of the Pennar/Krishna-Godavari River basins. This study highlights the deep history of the region and the importance of montane habitats as islands of unique biodiversity that have persisted through millions of years of changing climates. We describe three new species: Hemiphyllodactylus arakuensis sp. nov., H. jnana sp. nov. and H. kolliensis sp. nov. from montane habitats above 1000 m. The montane habitats of these species are emerging hotspots of reptile endemism, and this study emphasizes the need for systematic biodiversity inventory across India to uncover basic patterns of diversity and distribution. [ABSTRACT FROM AUTHOR]

Trichaline net-winged beetles (Lycidae: Metriorrhynchini) are a diverse group distributed in Australia, Wallacea and Indo-Burma. The phylogenetic relationships of ~120 taxa were recovered by applying maximum likelihood and Bayesian inference using DNA fragments of the cox1, rrnL and nad5 mitochondrial DNA and SSU and LSU ribosomal RNA genes. Divergence times and ancestral ranges were estimated using Bayesian approaches. We identified New Guinea as the ancestral region and estimated the date of dispersal events to continental Australia and Asia. Most Australian trichaline beetles diverged from New Guinean lineages during the Early Miocene to the Middle Miocene, and the fauna east of Lyddeker's Line was established by range expansion from New Guinea to the Moluccas, further on to the Philippines and then to the Greater Sunda Islands and Indo-Burma. A single species dispersed via the Lesser Sunda Islands to continental Asia. Trichaline beetles never crossed Wallace's Line between Sulawesi and Borneo. The dispersal westward started 20 Mya, after the first contact between Australian and Asian cratons, and three dispersal events led to the colonization of Sundaland. High genetic diversity and limited morphological diversification were identified in Oriental Diatrichalus and Microtrichalus, which colonized Indo-Burma during the last 5 Myr. Geographical isolation led to the origin of cryptic genetic diversity in Southeast Asia. [ABSTRACT FROM AUTHOR]

Aim: As a continental island, much of the biota of New Zealand was initially thought to have been shaped by vicariance. Recent studies, however, have highlighted the role of dispersal, with some even suggesting that the entire biota is the product of dispersal events following emergence of the islands. This study focuses on the interplay between dispersal and vicariance, specifically asking whether the spider family Orsolobidae has Gondwanan origins on New Zealand. Location: The spider family Orsolobidae was sampled from all continents where they occur (Africa, Australia, New Zealand and South America), comprising a total of 66 specimens representing the phylogenetic diversity of the family. Methods: DNA sequences were obtained from six fragments that were subsequently aligned and analysed with MrBayes3.2 and beast 1.8. The phylogeny was calibrated with fossils used as node calibrations, as well as with the substitution rate of Histone H3. Results: The orsolobid fauna of each land mass except Australia forms a monophyletic group in our analyses. The divergence dating analysis suggests that diversification of Orsolobidae started at a minimum of 80 Ma, while the New Zealand clade dates from a minimum of 40 Ma. Main conclusions: Thus, while many taxa have colonized the islands by dispersal, certain lineages, including the Orsolobidae, have clearly been capable of persisting through times of reduced land area. [ABSTRACT FROM AUTHOR]

Phylogenetic relationships in Calochilus (~30 species) were inferred based on a supermatrix of 81 loci including 22 species. To examine the spatio-temporal evolution of Calochilus , divergence-time estimations were conducted within a Bayesian framework using an uncorrelated relaxed molecular-clock model, followed by maximum-likelihood ancestral-range reconstructions comparing four biogeographic models. To trace the evolution of key floral and vegetative characters, maximum-likelihood ancestral-character reconstructions were carried out. The stem age of Calochilus was dated to ~12.0 million years ago in the mid-Miocene. Divergence of Calochilus into a tropical and a temperate clade was inferred to have occurred ~7.6 million years ago in the late Miocene. Northern Australia was reconstructed as the ancestral area of the tropical clade and the Euronotian region for the temperate clade. Range expansions from Australia to other Australasian regions, such as New Zealand and New Guinea, were inferred to have occurred only in recent geological times, commencing in the Pleistocene. The infrageneric classification for Calochilus was revised, erecting two subgenera, subgenus Calochilus and subgenus Tropichilus subgen. nov. Section Calochilus Szlach. was recircumscribed, and sect. Abrochilus sect. nov., and section Placochilus sect. nov. were erected. Identification keys to subgenera and sections and a taxonomic synopsis of the genus are provided. [ABSTRACT FROM AUTHOR]

Abstract The silvery mole-rat (Heliophobius argenteocinereus) is a solitary subterranean rodent with its distribution centred mainly in miombo woodlands of eastern Africa. This part of the continent was significantly influenced by the formation of the East African Rift System (EARS) during the last 25 Mya and by pronounced climatic changes in the Plio-Pleistocene that have caused genetic differentiation leading even to speciation events in many organisms. Recently, based on analysis of mitochondrial (mt) DNA sequences, it was suggested that H. argenteocinereus is a complex of six to eight species that diverged from the early to middle Miocene. In the present study, we significantly extended the sampling, re-analysed mtDNA datasets and analysed nuclear markers with the aim to assess the evolutionary history of Heliophobius. If we do not consider the old museum samples from south-eastern Democratic Republic of Congo (very divergent short mtDNA sequences obtained from ancient DNA, requiring further study from fresh material), the genus Heliophobius is composed of three major mtDNA lineages with parapatric distribution. The Rukwa Rift (+Mbeya triple junction) at the Zambia-Tanzania border, Lake Malawi, and the Eastern Arc Mountains form the biogeographical divides among these clades. The relatively shallow differences among the mitochondrial clades, divergence dating based on the use of the fossilised birth-death ratio model and a multi-locus dataset, and a very similar pattern of genetic structure to other rodents inhabiting the same area and habitat, suggest that the evolutionary history of the extant silvery mole-rat was predominantly influenced by the climatic fluctuations in the Plio-Pleistocene. Awaiting further studies employing genomic, ecological, morphological or behavioural data, we advocate for using the single name H. argenteocinereus for all evolutionary lineages within this taxon, because (1) comparison of the genetic structure observed in mtDNA and nuclear markers suggest hybridization between at least some mtDNA lineages in the contact zones; and (2) new samples close to the type localities suggest incorrect use of previous names. [ABSTRACT FROM AUTHOR]

Whereas most of the studies that discuss the evolutionary divergence of Anolis lizards have dated the clade’s crown group in between 31 and 64 Ma, a single study has recovered a significantly older age for the same node (87 Ma). These differences also entail notable consequences on the preferred biogeographical hypothesis for the whole clade. Here we analyze a total of seven dating strategies by combining three calibration sources in independent BEAST runs to infer the most probable divergence timing for anole lizards (a mitochondrial rate for ND2 gene, the Anolis dominicanus fossil, and a group of fossils assigned to the Priscagamines, Iguanines, and Idontosaurus clades). Based on the estimated timing, we also addressed whether chronograms differ the most in deeper or shallower nodes by exploring the trend in the standard deviation of mean ages between chronograms across time. Next, we focus on the pattern for a single shallow node by hypothesizing the biogeography of the island-endemic Malpelo anole ( Anolis agassizi ), and evaluating the temporal congruence between the species’ divergence and the island geology. The estimated set of ages suggests that anoles most likely diverged 72 Ma (71–73 Ma), with the crown group established around 58 Ma (51–65 Ma). Dispersal is therefore supported as the major driver in the biogeography of the group (and in Caribbean lineages in particular). Our analyses also indicated that (1) rate-based analyses pulled dates toward younger ages, (2) the differences in node ages between chronograms decrease towards the tips regardless of the position of the constrained node, and that (3) the estimated age for deep nodes (e.g. Anolis stem) is highly influenced when deep nodes are also constrained. The latter two results imply that the estimated age for shallower nodes is largely unaffected by the used temporal constraint. The congruence of all chronograms for the Malpelo anole also supports this finding. Anolis agassizi was found to have diverged before the emergence of Malpelo island in each analysis (anole: 19–31 Ma vs. Malpelo island: 16–17 Ma). Finally, we recommend when performing absolute dating analyses to first test for sequence saturation in the analyzed dataset (especially when calibrations are based on molecular rates). Our study also points out the importance of using multiple node constraints, especially when placed deeply in the tree, for fossil–based divergence dating analyses. [ABSTRACT FROM AUTHOR]

Premise of the Study: Recent estimates of crown ages for cycad genera (Late Miocene) challenge us to consider what processes have produced the extant diversity of this ancient group in such relatively little time. Pleistocene climate change has driven major shifts in species distributions in Mexico and may have led to speciation in the genus Dioon by forcing populations to migrate up in elevation, thereby becoming separated by topography. Methods: We inferred orthologs from transcriptomes of five species and sequenced these in 42 individuals representing all Dioon species. From these data and published plastid sequences, we inferred dated species trees and lineage‐specific diversification rates. Key Results: Analyses of 84 newly sequenced nuclear orthologs and published plastid data confirm four major clades within Dioon, all of Pleistocene age. Gene tree analysis, divergence dates, and an increase in diversification rate support very recent and rapid divergence of extant taxa. Conclusions: This study confirms the Pleistocene age of Dioon species and implicates Pleistocene climate change and established topography in lineage spitting. These results add to our understanding of the cycads as evolutionarily dynamic lineages, not relicts or evolutionary dead ends. We also find that well‐supported secondary calibration points can be reliable in the absence of fossils. Our hypothesis of lineage splitting mediated by habitat shifts may be applicable to other taxa that are restricted to elevation specific ecotones. [ABSTRACT FROM AUTHOR]

Abstract: Aim: Multiple geological and climatic events have created geographical or ecological barriers associated with speciation events, playing a role in biological diversification in Mexico. Here, we evaluate the influence of Neogene geological events and of Pleistocene climate change in the diversification of the genus Gerrhonotus using molecular dating and ancestral area reconstruction. Location: Mexico and south‐central United States. Methods: A multilocus sequence dataset was generated for 86 individuals of Gerrhonotus from most Mexican biogeographical provinces and belonging to five of the seven currently recognized species, as well as two putative undescribed species. Phylogeographical structure was explored using Poisson‐Tree‐Processes molecular species delimitation. Divergence events were estimated based on the fossil record using a relaxed uncorrelated lognormal clock. Ancestral areas were estimated at divergence events across the tree using a probabilistic Bayesian approach. Results: Extensive geographical structure was evident within three well‐supported clades. These clades probably diverged from each other in the early to mid‐Miocene, and their divergence was followed by six divergences in the late Miocene and eight divergences in the Pliocene. The ancestral origin of Gerrhonotus with keeled dorsal scales (keeled‐scale Gerrhonotus) was reconstructed to be across the Pacific Coast Province. Our phylogenetic analyses did not support the monophyly of Gerrhonotus. Main conclusions: Miocene and Pliocene geomorphology, perhaps in conjunction with climate change, appears to have induced allopatric divergence on a relatively small spatial scale in this genus. The late Miocene–Pliocene reduction in the highlands along the Tehuantepec fault probably created a large marine embayment that led to an early divergence in a clade of Gerrhonotus. Our analysis suggests uplifting of the Trans‐Mexican Volcanic Belt during this same time period resulted in additional diversification. This was followed by more recent, independent colonization events in the Pliocene from the Mexican Plateau to the Sierra Madre Oriental, Sierra Madre Occidental, Tamaulipas and Edwards Plateau provinces. A genus Gerrhonotus with the keeled‐scale species in addition to Coloptychon rhombifer (= G. rhombifer) is strongly supported. Inclusion of the smooth dorsal‐scale species in the genus is uncertain and maintained only tentatively. [ABSTRACT FROM AUTHOR]

Accurate species description in the marine environment is critical for estimating biodiversity and identifying genetically distinct stocks. Analysis of molecular data can potentially improve species delimitations because they are easily generated and independent, and yield consistent results with high statistical power. We used classical phylogenetic (maximum likelihood and Bayesian inference) and coalescent-based methods (divergence dating with fossil calibrations and coalescent-based species delimitation) to resolve the phylogeny of the spiny lobster Panulirus homarus subspecies complex in the Indo-West Pacific. Analyses of mitochondrial data and combined nuclear and mitochondrial data recovered Panulirus homarus homarus and Panulirus homarus rubellus as separately evolving lineages, while the nuclear data trees were unresolved. Divergence dating analysis also identified Panulirus homarus homarus and Panulirus homarus rubellus as two distinct clades which diverged from a common ancestor during the Oligocene, approximately 26 million years ago. Species delimitation using coalescent-based methods corroborated these findings. A long pelagic larval life stage and the influence of ocean currents on post-larval settlement patterns suggest that a parapatric mode of speciation drives evolution in this subspecies complex. In combination, the results indicate that Panulirus homarus rubellus from the Southwest Indian Ocean is a separately evolving lineage and possibly a separate species.

Background: Recent studies have begun to reveal the complex evolutionary and biogeographic histories of mainland anoles in Central America, but the origins and relationships of many taxa remain poorly understood. One such group is the Anolis (Norops) crassulus species subgroup, which contains ten morphologically similar highland taxa, the majority of which have restricted distributions. The nominal taxon A. crassulus has a disjunct distribution from Chiapas, Mexico, through Guatemala, in the highlands of El Salvador, and in the Chortís Highlands of Honduras. We test the relationships of these species using multiple mitochondrial and nuclear loci in concatenated and multispecies coalescent frameworks, in an effort to both resolve long-standing taxonomic confusion and present new insights into the evolution and biogeography of these taxa. Results: Sequences of multiple mitochondrial and nuclear loci were generated for eight of the ten species of the Anolis crassulus species subgroup. We analyzed phylogenetic relationships and estimated divergence times and ancestral ranges of the subgroup, recovering a monophyletic subgroup within Anolis. Within the nominal taxon Anolis crassulus, we recovered multiple genetically distinct lineages corresponding to allopatric populations, and show that the Chortís Highland lineage split from the others over 13 MYA. Additionally, distinct mitochondrial lineages are present within the taxa A. heteropholidotus and A. morazani, and importantly, samples of A. crassulus and A. sminthus previously used in major anole phylogenetic analyses are not recovered as conspecific with those taxa. We infer a Chortís Highland origin for the ancestor of this subgroup, and estimate cladogenesis of this subgroup began approximately 22 MYA. Conclusions: Our results provide new insights into the evolution, biogeography, and timing of diversification of the Anolis crassulus species subgroup. The disjunctly distributed Anolis crassulus sensu lato represents several morphologically conserved, molecularly distinct anoles, and several other species in the subgroup contain multiple isolated lineages. [ABSTRACT FROM AUTHOR]

The phylogenetic relationships and biogeographic history of Caribbean island ameivas ( Pholidoscelis) are not well-known because of incomplete sampling, conflicting datasets, and poor support for many clades. Here, we use phylogenomic and mitochondrial DNA datasets to reconstruct a well-supported phylogeny and assess historical colonization patterns in the group. We obtained sequence data from 316 nuclear loci and one mitochondrial marker for 16 of 19 extant species of the Caribbean endemic genus Pholidoscelis. Phylogenetic analyses were carried out using both concatenation and species tree approaches. To estimate divergence times, we used fossil teiids to calibrate a timetree which was used to elucidate the historical biogeography of these lizards. All phylogenetic analyses recovered four well-supported species groups (clades) recognized previously and supported novel relationships of those groups, including a ( P. auberi + P. lineolatus) clade (western + central Caribbean), and a ( P. exsul + P. plei) clade (eastern Caribbean). Divergence between Pholidoscelis and its sister clade was estimated to have occurred ~25 Ma, with subsequent diversification on Caribbean islands occurring over the last 11 Myr. Of the six models compared in the biogeographic analyses, the scenario which considered the distance among islands and allowed dispersal in all directions best fit the data. These reconstructions suggest that the ancestor of this group colonized either Hispaniola or Puerto Rico from Middle America. We provide a well-supported phylogeny of Pholidoscelis with novel relationships not reported in previous studies that were based on significantly smaller datasets. We propose that Pholidoscelis colonized the eastern Greater Antilles from Middle America based on our biogeographic analysis, phylogeny, and divergence time estimates. The closing of the Central American Seaway and subsequent formation of the modern Atlantic meridional overturning circulation may have promoted dispersal in this group. [ABSTRACT FROM AUTHOR]

The Eastern Arc Mountains (EAM) have long been recognized as an area of extraordinary endemic biodiversity but have remained understudied compared to other biodiversity hotspots. The tribelocephaline assassin bug genus Xenocaucus China & Usinger, 1949, currently comprises two species known from the Uluguru Mountains of the EAM and Bioko Island in the Gulf of Guinea. Both species are based on single apterous and apparently eyeless female specimens. Based on collections resulting from extensive leaf litter sampling in Tanzania and Ethiopia, we here describe six new species, five based on females ( Xenocaucus chomensis, n. sp., Xenocaucus kimbozensis, n. sp., Xenocaucus nguru, n. sp., Xenocaucus rubeho, n. sp., and Xenocaucus uluguru, n. sp.) and Xenocaucus ethiopiensis, n. sp., for which we discovered a macropterous male with well-developed eyes in addition to the apterous females. Molecular phylogenetic analyses indicate that Xenocaucus ethiopiensis, n. sp., is the sister taxon to the Tanzanian clade and support morphology-based species concepts. Divergence dating shows that diversification in the Tanzanian clade started ∼15 mya, with the youngest species-level split occurring ∼8 mya. Three species occur across multiple mountain ranges in the EAM or occur also on Mt. Hanang, and biogeographic analyses suggest a complex history of Xenocaucus in East Africa. [ABSTRACT FROM AUTHOR]

Kingsnakes of the Lampropeltis getula complex range throughout much of temperate and subtropical North America. Studies over the last century have used morphology and color pattern to describe numerous subspecies. More recently, DNA analyses have made invaluable contributions to our understanding of their evolution and taxonomy. We use genetic and ecological methods to test previous hypotheses of distinct evolutionary lineages by examining 66 total snakes and 1) analyzing phylogeographic structure using 2 mtDNA loci and 1 nuclear locus, 2) estimating divergence dates and historical demography among lineages in a Bayesian coalescent framework, and 3) applying ecological niche modeling (ENM). Our molecular data and ENMs illustrate that 3 previously recognized subspecies in the eastern United States comprise well-supported monophyletic lineages that diverged during the Pleistocene. The geographic boundaries of these 3 lineages correspond closely to known biogeographic barriers (Florida peninsula, Appalachian Mountains, and Apalachicola River) previously identified for other plants and animals, indicating shared geographic influences on evolutionary history. We conclude that genetic, ecological, and morphological data support recognition of these 3 lineages as distinct species (Lampropeltis floridana, Lampropeltis getula, and Lampropeltis meansi). [ABSTRACT FROM AUTHOR]