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Contrasting phylogeographic histories between the continent and islands of East Asia: Massive mitochondrial introgression and long-term isolation of hares (Lagomorpha: Lepus)
... bPTP species delimitation, which integrates both nuclear and mi- (Kinoshita et al., 2019;Sato, 2016). ...
... Second, although some continental archipelagos were historically ice-covered through glacial maxima, others served as ice-free refugia that enabled geographically isolated persistence and divergence of peripheral terrestrial populations through ice ages (Byun et al., 1997;Kinoshita et al., 2019;Shafer et al., 2010). Together, episodic vicariance and connectivity, shaped by both climate and geographic complexity, have combined to produced elevated levels of insular endemism in continental archipelagos, despite their proximity to mainland source populations (Patiño et al., 2017; Alexander Archipelago, Alaska, USA, Dawson et al., 2007, Sawyer et al., 2019Canary Islands, Spain, Caujapé-Castells et al., 2017;Haida Gwaii, British Columbia, Canada, Foster, 1965;Japanese Archipelago, Sato, 2016). ...
... In contrast, genetic similarity be- et al., 1999Sato, 2016). Similar distributional and introgression patterns have been observed in hare of the genus Lepus (Kinoshita et al., 2019). Introgression coincident with climatic cycling has been identified among east Asian mountain hares (Lepus timidus) ...
Aim
Refugial isolation during glaciation is an established driver of speciation; however, the opposing role of interglacial population expansion, secondary contact, and gene flow on the diversification process remains less understood. The consequences of glacial cycling on diversity are complex and especially so for archipelago species, which experience dramatic fluctuations in connectivity in response to both lower sea levels during glacial events and increased fragmentation during glacial recession. We test whether extended refugial isolation has led to the divergence of genetically and morphologically distinct species within Holarctic ermine (Mustela erminea), a small cosmopolitan carnivore species that harbours 34 extant subspecies, 14 of which are insular endemics.
Location
Holarctic.
Methods
We use genetic sequences (complete mitochondrial genomes, four nuclear genes) from >100 ermine (stoats) and geometric morphometric data for >200 individuals (27 of the 34 extant subspecies) from across their Holarctic range to provide an integrative perspective on diversification and endemism across this complex landscape. Multiple species delimitation methods (iBPP, bPTP) assessed congruence between morphometric and genetic data.
Results
Our results support the recognition of at least three species within the M. erminea complex, coincident with three of four genetic clades, tied to diversification in separate glacial refugia. We found substantial geographic variation within each species, with geometric morphometric results largely consistent with historical infraspecific taxonomy.
Main conclusions
Phylogeographic structure mirrors patterns of diversification in other Holarctic species, with a major Nearctic‐Palearctic split, but with greater intraspecific morphological diversity. Recognition of insular endemic species M. haidarum is consistent with a deep history of refugial persistence and highlights the urgency of mindful management of island populations along North America's North Pacific Coast. Significant environmental modification (e.g. industrial‐scale logging, mining) has been proposed for a number of these islands, which may elevate the risk of extinction of insular palaeoendemics.
... 5 and 6) with a few microsatellite loci. This could be explained by the theory of nuclear-mitochondrial discordance (Lu et al., 2001;Walsh et al., 2016;Haines et al., 2017;Kinoshita et al., 2019). This phenomenon among birds is probably related to several factors, such as sex-biased dispersal pattern (Toews & Brelsford, 2012;Dai et al., 2013), distribution changes (Seixas et al., 2018), and simple stochastic variation in coalescence times across loci (Rosenberg, 2003;Phuong et al., 2017). ...
... Hybridization or introgression between species occurs frequently (more than 9%) among birds (Grant & Grant, 1992;Randler, 2002;Mallet, 2005;Vigfusdottir et al., 2008;Wang et al., 2014;Walsh et al., 2016;Hanna et al., 2018). Recently, several studies have shown that when reconstructing phylogenetic relationships among related species, introgression might exacerbate nuclearmitochondrial discordance (Lu et al., 2001;Walsh et al., 2016;Haines et al., 2017;Kinoshita et al., 2019). Another alternative cause for nuclear-mitochondrial discordance might be incomplete lineage sorting due to the fourfold difference in effective population size between the mtDNA and nuclear loci. ...
Species are the basic units in evolution and biodiversity and thus a reasonable species classification is essential to assess and protect biodiversity. The classifications of the Naumann’s and dusky thrush complexes and the red-throated and black-throated thrush complexes are not well defined in Turdidae (Aves, Passeriformes). Herein, we use qualitative and quantitative morphological characters and molecular data to review the taxonomy of these thrush complexes. These four thrushes can be distinguished with qualitative features of feather color and striping. These birds cannot be divided by quantitative features, which only work on two groups of thrush complexes. Phylogenetic analysis based on mitochondrial genes indicate that all haplotypes might be divided into two monophyletic clades corresponding to two groups of thrush complexes. According to coalescence-based species delimitation and the gen-morph species concept, these two groups of thrush complexes should be separated as two distinctive species (T. naumanni and T. ruficollis) and including two subspecies per species. This species classification is also supported by gene flow analysis. There is a significant mixing between these two thrush species in the neighbor-joining (NJ) tree and the cluster analysis using a few microsatellite loci. This leads to a pattern of nuclear-mitochondrial discordance between the two birds that can be explained by several potential mechanisms. This study provides the first comprehensive classification of the two thrush complexes on a population level using morphological and molecular characteristics, which will be useful in expanding our understanding of species division among thrush complexes.
... viridis viridis zone (Pons et al., 2019), to moderate introgression (e.g., voles Microtus californicus; Lin et al., 2018) and massive introgression (e.g., hares Lepus timidus/L. mandshuricus; Kinoshita et al., 2019). The extreme is "mitochondrial capture"-the complete mt genome replacement (e.g., between buntings Emberiza citrinella and E. leucocephalos; Irwin et al., 2009). ...
... mtDNA is usually much more prone to be maintained in a population after introgression than nuclear genes (Kinoshita et al., 2019;Lin et al., 2018;Pons et al., 2014;Renoult et al., 2009). In our case, however, introgression was detected based on nuclear genes, rather than mitochondrial markers, strongly indicating predominantly male-biased dispersal in magpies. ...
Zones of secondary contact provide a good opportunity to investigate the origin and dynamics of reproductive isolation between related populations. We analyzed genetic and phenotypic patterns and gene flow between two subspecies of the Eurasian magpie Pica pica s.l. which recently came into contact after presumably long periods of isolation. We describe the distribution of subspecies in a young contact zone at Argun’ river basin in southern Siberia where populations occur in parapatry and an older hybrid population in eastern Mongolia. Based on genome-wide SNP data, we analyzed patterns and strength of gene flow between the subspecies. Our results indicate occasional hybridization with backcrossing and asymmet- ric introgression along a wide range in Transbaikalia and locally in eastern Mongolia. Males of P. p. jankowskii apparently exhibit higher dispersal ability towards the west compared to P. p. leucoptera (towards the east). The former occasionally migrates to eastern Mongolia and Transbaikalia where introgression of nuclear, but not mitochondrial DNA was evident. Bioacoustic investigations showed differences between the subspecies in speed and structure of vocalization. We discovered intermediate calls of hybrid magpies and bilingual birds alternating calls that are typical for the two taxa. Furthermore, we found dramatically decreased reproductive success in hybridogeneous populations. By complementing our results with established phylogeographic patterns of P. pica s.l. based on a mitochondrial marker sequence, and considering indications of sterility of hybrids in the contact zone, we propose to elevate the two corresponding subspecies to species level: P. pica for the western form and P. serica for the eastern form.
... argentatus in Iceland (Vigfusdottir et al., 2008),Aegithalos bonvaloti and A. fuliginosus in southwestern China (Wang et al., 2014), Ammodramus caudacutus and A. nelsoni on the northeastern coast of the United States (Walsh et al., 2016), and Strix varia and S. occidentalis in western North America (Hanna et al., 2018). Recently, some studies have shown that when reconstructing phylogenetic relationships among related species, introgression might exacerbate nuclear-mitochondrial discordance (Haines et al., 2017;Kinoshita et al., 2019;Lu et al., 2001;Walsh et al., 2016). There are several possible hypotheses to explain these phenomena among birds, such as sex bias (Dai et al., 2013;Toews and Brelsford, 2012), distribution changes (Seixas et al., 2018), and simple stochastic variation in coalescence times across loci (Phuong et al., 2017;Rosenberg, 2003). ...
... The recent interspecies crossing between T. naumanni and T. ruficollis might have resulted in significant nuclear introgression. Although the introgression of mitochondrial genes is more common in nature (Aboim et al., 2010;Kinoshita et al., 2019;Mao et al., 2013), nuclear introgression is also present in birds. Nuclear introgression mainly relies on male-biased gene flow. ...
The classification of some Turdus species, such as the Naumann’s and dusky thrush complexes and the red-throated and black-throated thrush complexes, is controversial. Herein, we used molecular data (mitochondrial genes and microsatellite loci) and morphological characters to review the taxonomy of these thrush complexes and analyze the genetic differentiation between them. Our phylogenetic analysis based on mitochondrial genes indicated that all haplotypes could be divided into two reciprocally monophyletic sister clades corresponding to these two thrush complexes. The same results were revealed by coalescence-based species delimitation. Therefore, these two thrush complexes should be divided into two separate species (T. naumanni and T. ruficollis) and include two subspecies per species according to combined characters from morphological analyses and multilocus approaches. The above classifications were also supported by an analysis of genetic differentiation between T. naumanni and T. ruficollis and within each species. Moreover, there was significant mixing between these two thrush species in the neighbor-joining (NJ) tree and the cluster analysis of microsatellite loci. This led to a pattern of nuclear-mitochondrial discordance between the two species. This could be the result of extensive nuclear introgression between these two sister species. We also provide a potential explanation for the mechanism of gene introgression and nuclear-mitochondrial discordance between the two bird species.
... This shift is reliable; i.e., confidence interval of the cline for cytb does not overlap with the intervals of other markers (the only exception is the cline for tp53 of the "Nizhny Novgorod" transect) ( Table 3). This phenomenon is in full accordance with the results of simulation modeling [30,31], field experiments [32], and studies of real natural situations [33][34][35][36], according to which, when one species invades the range of another, the direction of mtDNA introgression is opposite to the direction of dispersal. When studying the behavior of males of M. arvalis and M. obscurus in the "partition" and "open field" tests, it was found that males of M. obscurus more active in exploring new territory than males of M. arvalis [37,38]. ...
Patterns of introgression of several genetic markers across the hybrid zone between allied species of the common vole Microtus arvalis s. str. and M. obscurus was studied in four of its sections: in northwest Nizhny Novgorod oblast, east Vladimir and southwest Nizhny Novgorod oblasts, south Lipetsk oblast, and northwest Voronezh oblast. Analysis of the clinal variability for three molecular genetic markers (cytb, tp53, SMCY11) and for karyotypes showed a structural similarity between the "Vladimir-Nizhny Novgorod," "Nizhny Novgorod," and "Voronezh" sections. The maximum width was shown for the cytb cline; the minimum width was shown for the SMCY11 cline; the tp53 cline and chromosomal cline occupy an intermediate position for this parameter. Furthermore, in these transects, the center of the cline for the cytb is shifted southeastward (into the distribution range of M. obscurus) from the centers of three other clines. The revealed asymmetric introgression of mitochondrial genome from M. arvalis to M. obscurus may be explained by the fact that the hybrid zone was formed as a result of invasion of M. obscurus into the range of M. arvalis. The "Lipetsk" transect differs from the three above-mentioned transects in very narrow clines with nearly coinciding centers. Such characteristics of the "Lipetsk" transect are obviously caused by localization of the hybrid zone in this section along Voronezh River. The obtained results led us to suppose that the structure of the studied hybrid zone is determined mainly by coincidence (or noncoincidence) of its center with local physical barriers.
... Unique genetic diversity of the Hokkaido sable, shaped by repeated isolation and admixture as observed in this study, possibly with ancestral polymorphism and/or ancient introgression (Ishida et al., 2013), could have contributed to long-term persistence and local adaptation on the island. In previous studies of the mountain hare (Kinoshita et al., 2019) and brown bear (de Jong et al., 2023), ...
Aim: The continental island system comprising Sakhalin, Hokkaido and the southern
Kuril Islands (SHSK) in northeastern Asia serves as one of the southernmost habitats
for many boreal and arctic organisms, with colonization via land bridges formed during glacial periods. To understand the impacts of past land-bridge formation under Quaternary climate changes across SHSK, we investigated the demographic history of forest-dwelling marten species.
Location: Sakhalin, Hokkaido and the southern Kuril Islands in northeastern Asia.
Taxon: Sable, Martes zibellina (Carnivora, Mustelidae).
Methods: We employed multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq) to obtain genome-wide single nucleotide polymorphisms (SNPs). We tested possible scenarios of colonization and diversification for SHSK sables using several population genetics approaches including clustering analysis, population tree estimation and approximate Bayesian computation modelling. We also examined haplotype diversity for the mitochondrial ND2 gene.
Results: The genetic diversity of the island populations and their affinity for continental populations were found to be higher in the order Sakhalin > Hokkaido > Iturup in both nuclear SNP and mitochondrial DNA analyses. Demographic analyses indicated that the sable migrated repeatedly from the continent, particularly to the neighbouring Sakhalin Island. However, only an earlier colonized lineage has persisted on marginal Iturup Island since the Middle Pleistocene. The stronger effects of repeated migrations and/or isolation influenced by the distance to the continent have shaped the contemporary genetic diversity and differentiation of sable populations in SHSK.
Main Conclusions: Genome-wide and comprehensive sampling approaches demonstrated that the forest-dwelling sable had long-term persistence with partial admixture of multiple lineages in SHSK, suggesting the existence of forest corridors
and refugia on the islands during the last several glacial periods. The SHSK system of continental islands is valuable for understanding the impacts of Quaternary climate changes on the genetic diversity and evolutionary histories of boreal organisms.
... Extensive barcoding from a previous study ( Supplementary Fig. S2) (Zhang et al., 2017) provide evidence of interspecies mtDNA introgression between C. punctiger and C. graminis. Introgression has been increasingly reported across a wide range of species groups and even between sister taxa (Funk and Omland, 2003;Kinoshita et al., 2019;Taylor et al., 2021). ...
Accurate taxonomy and delimitation are of great importance for pest control strategies and management programs. Here, we focus on Cletus (Insecta: Hemiptera: Coreidae), which includes many crop pests. The species boundaries still conflict and only cytochrome c oxidase subunit I (COI) barcoding has been previously used for molecular studies. We generated new mitochondrial genome and nuclear genome-wide SNPs to explore the species boundaries of 46 Cletus samples from China using multiple species delimitation approaches. All results recovered a monophyly with high support, except for two closely related species in clade I - C. punctiger and C. graminis. Mitochondrial data demonstrated admixture in clade I, while genome-wide SNPs unambiguously identified two separate species, which were confirmed by morphological classification. Inconsistent nuclear and mitochondrial data indicated mito-nuclear discordance. Mitochondrial introgression is the most likely explanation, and more extensive sampling and more comprehensive data are needed to ascertain a pattern. Accurate species delimitation will shed light on species status; thus, an accurate taxonomy is of particular concern, as there is a pressing need to implement precise control of agricultural pests and to perform further research on diversification.
... In East Asia, the genesis and historical and evolutionary dynamics of many species with discontinuous distributions have been studied using phylogenetic methods [8,11]. The barriers between the East China Sea and the Korea Strait have played a vital role in genetic differentiation between populations [12][13][14][15], and the Donghai and Korea Strait land bridges have provided corridors during dispersal and migration of both plants and animals [8,9,[16][17][18]. RAPD (random amplified polymorphic DNA), AFLP (amplified fragment length polymorphism), and SSR (simple sequence repeats or microsatellites) were primarily used as molecular markers in these earlier studies. ...
The study of population genetic structure and historical dynamics of species with disjunct distribution can reveal the mechanisms through with they were formed. Pinus densiflora is an essential tree species with ecological and economic value, and its natural distribution shows a disjunct pattern. Using transcriptome-level SNP data from 220 samples representing 32 naturally-distributed populations in East Asia, we investigated Pinus densiflora genetic diversity and structure, divergence time, and ancestral distribution. We identified five subpopulations which diverged approximately 2.02–1.49 million years ago, and found relatively low genetic differentiation among the three large subpopulations (SL, JH, and JK). Northeast China is the most likely origin, and its current distribution is the result of dispersal and vicariance events. It migrated southwest through the Liaodong Peninsula to the Shandong Peninsula and southeast through the Korean Peninsula to Japan. These results provide a basis for the conservation and management of P. densiflora in the future and the evolutionary study of species with similar life histories.
... Hybridisation and introgression are ubiquitous throughout the genus Lepus and throughout their distribution and involve ancient as well as recent phenomena (Alves et al. 2003;Liu et al. 2011;Acevedo et al. 2012;Melo-Ferreira et al. 2014a, b;Marques et al. 2017a;Seixas et al. 2018;Ashrafzadeh et al. 2018;Momhammadi et al. 2020). Phylogenetic or deep introgression is associated with species replacements during glacial advances and retreats (Melo-Ferreira et al. 2014c;Kinoshita et al. 2019). More recent introgression occurs where there are parapatric distributions, perhaps leading to a hybrid zone, or species expansions due to climate change or introductions (Zachos et al. 2010;Cheng et al. 2014;Schenker et al. 2020). ...
Introduced non-native species can threaten native species through interspecific hybridisation and genetic introgression. We assessed the prevalence of hybridisation and introgression between introduced European brown hare, Lepus europaeus , and the endemic Irish hare, L. timidus hibernicus . Roadkill hares ( n = 56) were sequenced for a 379bp section of the mitochondrial DNA D-loop and a 474bp segment of the nuclear transferrin ( Tf ) gene. A species-specific indel in the transferrin gene was present in L.t. hibernicus and absent in L. europaeus . Excluding three hares from which molecular data could not be recovered, 28 hares (53%) were native L.t. hibernicus , 7 (13%) were non-native L. europaeus and 18 (34%) were hybrids; of which 5 (28%) were first generation (F1) involving bidirectional crosses with mismatched nuclear and mtDNA (3 ♂ europaeus x ♀ hibernicus and 2 ♂ hibernicus x ♀ europaeus ). Mixed nuclear transferrin sequences suggested 13 (72%) of hybrids were at least 2nd generation (F2) with 9 (69%) possessing L.t. hibernicus and 4 (31%) L. europaeus mtDNA (the latter indicative of hybrid backcrossing with the non-native). The prevalence of hybridisation at similar mountain-brown hare contact zones throughout Europe is notably lower (4–16%) and typically unidirectional (♂ europaeus x ♀ timidus ). A high prevalence of bidirectional hybridisation and introgression (in association with projected climate change) may favour the introduced species over the native. Genetic surveillance and population monitoring are needed to further explore the potential conservation implications of European brown hare in Ireland.
... However, our study was the first comprehensive phylogenetic analysis of Pinellia at the cp genome level, and the resulting topologies based on either whole cp genome or CDS datasets both definitively show that P. pedatisecta cannot be the ancestor of Pinellia species. The main habitat of all three Pinellia species in our study is in the southeastern portion of Asia, where hybridization and introgression have been reported [55,56], which may cause interspecific gene flow in response to ecological selection and lead to difficulties in molecular phylogenetic analysis. Given that the cp and nuclear genomes evolve independently, the phylogeny of cp genomes alone is insufficient in making taxonomic decisions about Pinellia. ...
Background
Pinellia Tenore (Araceae) is a genus of perennial herbaceous plants, all of which have medicinal value. The chloroplast (cp) genome data of Pinellia are scarce, and the phylogenetic relationship and gene evolution remain unclear.
Methods and results
We sequenced and annotated the Pinellia pedatisecta cp genome and combined it with previously published genomes for other Pinellia species. We used bioinformatics methods to analyse the genomic structure, repetitive sequences, interspecific variation, divergence hotspots, phylogenetic relationships, divergence time estimation and selective pressure of four Pinellia plastomes. Results showed that the cp genomes of Pinellia varied in length between 168,178 (P. pedatisecta MN046890) and 164,013 bp (P. ternata KR270823). A total of 68–111 SSR loci were identified as candidate molecular markers for further genetic diversity study. Eight mutational hotspot regions were determined, including psbI-trnG-UCC, psbM-rpoB, ndhJ-trnT-UGU, trnP-UGG-trnW-CCA, ndhF-trnN-GUU, ndhG-ndhE, ycf1-rps15 and trnR-ycf1. Gene selection pressure suggested that four genes were subjected to positive selection. Phylogenetic inferences based on the complete cp genomes revealed a sister relationship between Pinellia and Arisaema plants whose divergence was estimated to occur around 22.48 million years ago. All Pinellia species formed a monophyletic evolutionary clade in which P. peltata, rather than P. pedatisecta, earlier diverged, indicating that P. pedatisecta is not the basal taxon of Pinellia but P. peltata may be.
Conclusions
The cp genomes of Pinellia will provide valuable information for species classification, identification, molecular breeding and evolutionary exploration of the genus Pinellia.
... However, our study was the rst comprehensive phylogenetic analysis of Pinellia at the cp genome level, and the resulting topologies based on either whole cp genome or CDS datasets both de nitively show that P. pedatisecta cannot be the ancestor of Pinellia plants. The main habitat of all three Pinellia species in our study is in the southeastern portion of Asia, where hybridization and introgression have been reported [49,50], which may cause interspeci c gene ow in response to ecological selection and lead to di culties in molecular phylogenetic analysis. Given that the cp and nuclear genomes evolve independently, the phylogeny of cp genomes alone is insu cient in making taxonomic decisions about Pinellia. ...
Background Pinellia Tenore (Araceae) is a genus of perennial herbaceous plants, all of which have medicinal value. The chloroplast (cp) genome data of Pinellia are scarce, and the phylogenetic relationship and gene evolution remain unclear.
Methods and results In this study, we sequenced and annotated the Pinellia pedatisecta cp genome and combined it with previously published genomes for other Pinellia species. We used bioinformatics methods to analyse the genomic structure, repetitive sequences, interspecific variation, divergence hotspots, phylogenetic relationships, divergence time estimation and selective pressure of four Pinellia plastomes. Results showed that the cp genomes of Pinellia varied in length between 168,178 (P. pedatisecta MN046890) and 164,013 bp (P. ternata KR270823). A total of 68–111 SSR loci were identified as candidate molecular markers for further genetic diversity study. Eight mutational hotspot regions were determined, including psbI-trnG-UCC, psbM-rpoB, ndhJ-trnT-UGU, trnP-UGG-trnW-CCA, ndhF-trnN-GUU, ndhG-ndhE, ycf1-rps15 and trnR-ycf1. Gene selection pressure suggested that four genes were subjected to positive selection. Phylogenetic inferences based on the complete cp genomes and their protein-coding sequences revealed a sister relationship between Pinellia and Arisaema plants whose divergence was estimated to occur around 22.48 million years ago. All Pinellia plants formed a monophyletic evolutionary clade in which P. peltata, rather than P. pedatisecta, earlier diverged, indicating that P. pedatisecta is not the basal taxon of Pinellia but P. peltata may be.
Conclusions The cp genomes of Pinellia will provide valuable information for species classification, identification, molecular breeding and evolutionary exploration of the genus Pinellia.
... Recent studies based on exome of the whole genome supported five subgenera of extant Ochotona: Alienauroa, Conothoa, Ochotona, Lagotona, and Pika, with divergence time and phylogeographic analyses inferring the last common ancestor of extant pikas first occurred in the middle Miocene, approximately 14 Ma (Wang et al., 2020). Mito-nuclear discordance was shown in Lepus (Kinoshita et al., 2019) and Ochotona (Lissovsky et al., 2019), which could be the result of incomplete lineage sorting, sex-biased dispersal, asymmetrical introgression, natural selection, or Wolbachiamediated genetic sweeps. The genome of four lagomorph species (O. ...
Due to their global distribution, invasive history, and unique characteristics, European rabbits are recognizable almost anywhere on our planet. Although they are members of a much larger group of living and extinct mammals [Mammalia, Lagomorpha (rabbits, hares, and pikas)], the group is often characterized by several well-known genera (e.g., Oryctolagus, Sylvilagus, Lepus, and Ochotona). This representation does not capture the extraordinary diversity of behavior and form found throughout the order. Model organisms are commonly used as exemplars for biological research, but there are a limited number of model clades or lineages that have been used to study evolutionary morphology in a more explicitly comparative way. We present this review paper to show that lagomorphs are a strong system in which to study macro- and micro-scale patterns of morphological change within a clade that offers underappreciated levels of diversity. To this end, we offer a summary of the status of relevant aspects of lagomorph biology.
... Cp-genome (chloroplast genome) possess a highly conserved tetrad structure, containing two inverted repeat (IR) regions (IRa and IRb), a small single-copy (SSC) region and a large single-copy (LSC) region [19][20]. In addition to photosynthesis, cp genome-encoded proteins are involved in other metabolic processes, such as responses to heat, drought, salt, and light [21]. ...
Magnolia officinalis , M. officinalis sub s p. biloba and M. hypoleuca are all typical medicinal plants, belonging to genus Magnolia and Family Magnoliaceae. Their molecular information, particularly genetic difference, were known less. In this study, the platform Illumina HiSeq was used to sequence and assemble a novel cp (chloroplast) genome of M . hypoleuca followed by cp purification. Combined with two published cp rawdata, gene cycles and function annotations were comparably performed for the three plant species. The results indicated that 19 791 019 clean reads was assembled for M . hypoleuca cp, Q30 being 91.33%, and genome 160 051 bp. Its GC content is 39.2%, including 37 tRNAs and 8 rRNAs. The M. hypoleuca had smaller chloroplast genome and more introns (or exons) than M. officinalis and M. officinalis sub s p. biloba . And there were respectively 11 and 8 more functional genes in M . hypoleuca cp than that in the other two. Based on cp complete genomes sequences, we constructed the phylogenetic relationship and estimated the divergence time of the three species by ML (Maximum likelihood) method, with other 10 published Magnoliaceae species. The results showed that M. officinalis sub s p. biloba and M. officinalis might diverge from M. hypoleuca around 18.98 Ma, then they diverged from each other around 15.00 Ma. Additionally, the middle Miocene warming period might play an important role in the demographic and evolutionary histories of the three Magnolias, which provided a novel insight of the origin and dispersal routes of M . hypoleuca .
... Hares are primarily associated with open grasslands, but can be found across a broad range of biomes (e.g., desert, forest, or arctic) and elevations (e.g., from sea level to the Himalayan or Ethiopian plateau; Smith et al., 2018). The Lepus radiation also provides multiple case studies of hybridization and introgression, with admixture detected among several extant pairs of species (e.g., Liu et al. 2011;Melo-Ferreira et al. 2012;Tolesa et al. 2017;Jones et al. 2018;Seixas et al. 2018;Lado et al. 2019;Kinoshita et al. 2019). Selection on introgressed variation has been hypothesized to have aided the range expansion of the Iberian hare (Seixas et al. 2018), and has been directly linked to convergent adaptive evolution of non-white winter coats in populations of two species that change the color of their pelage seasonally (Jones et al. 2018(Jones et al. , 2020aGiska et al. 2019). ...
Hybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares (Lepus) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification of Lepus, we analyzed whole exome sequences (61.7 Mb) from 15 species of hares (1- 4 individuals per species), spanning the global distribution of the genus, and two outgroups. We used a coalescent framework to infer species relationships and divergence times, despite extensive genealogical discordance. We found high levels of allele sharing among species and show that this reflects extensive incomplete lineage sorting and temporally layered hybridization. Our results revealed recurrent introgression at all stages along the Lepus radiation, including recent gene flow between extant species since the last glacial maximum, but also pervasive ancient introgression occurring since near the origin of the hare lineages. We show that ancient hybridization between northern hemisphere species has resulted in shared variation of potential adaptive relevance to highly seasonal environments, including genes involved in circadian rhythm regulation, pigmentation, and thermoregulation. Our results illustrate how the genetic legacy of ancestral hybridization may persist across a radiation, leaving a long-lasting signature of shared genetic variation that may contribute to adaptation.
... Hares are primarily associated with open grasslands, but can be found across a broad range of biomes (e.g., desert, forest, or arctic) and elevations (e.g., from sea level to the Himalayan or Ethiopian plateau; Smith et al. 2018). The Lepus radiation also provides multiple case studies of hybridization and introgression, with admixture detected among several extant pairs of species (e.g., Liu et al. 2011;Melo-Ferreira et al. 2012;Tolesa et al. 2017;Jones et al. 2018;Seixas et al. 2018;Lado et al. 2019;Kinoshita et al. 2019). Selection on introgressed variation has been hypothesized to have aided the range expansion of the Iberian hare (Seixas et al. 2018) and has been directly linked to convergent adaptive evolution of nonwhite winter coats in populations of two species that change the color of their pelage seasonally (Jones et al. 2018(Jones et al. , 2020aGiska et al. 2019). ...
... The underlying reason for this mito-nuclear discordance is yet to be tested, but introgression could be a plausible hypothesis. Mito- nuclear discordance is quite common among mammals, and is often attributed to mitochondrial introgression, for example in voles (Boratyński et al., 2011;Bastos-Silveira et al., 2012), in chipmunks (Sarver et al., 2016) and in hares (Alves et al., 2008;Boratyński et al., 2011;Kinoshita et al., 2019). Sex-biased dispersal, such as that observed in the slit-faced bats, Nycteris thebaica (Demos et al., 2019), could also explain this discordance, although there is no evidence for sex-biased dispersal in A. hottentotus. ...
Golden moles (Family Chrysochloridae) are small subterranean mammals, endemic to sub-Saharan Africa, and many of the 21 species are listed as threatened on the IUCN Red List. Most species have highly restricted ranges; however two species, the Hottentot golden mole (Amblysomus hottentotus) and the Cape golden mole (Chrysochloris asiatica) have relatively wide ranges. We recently uncovered cryptic diversity within A. hottentotus, through a phylogeographic analysis of this taxon using two mitochondrial gene regions and a nuclear intron. To further investigate this cryptic diversity, we generated nuclear SNP data from across the genome of A. hottentotus, by means of double-digest restriction-site associated DNA sequencing (ddRADSeq), and mapped reads to the Cape golden mole genome. We conducted a phylogenetic analysis and investigated population differentiation. Our results support the distinctiveness of A. h. meesteri. Furthermore, we provide evidence from nuclear SNPs in support of our previous finding that Central coastal samples represent a unique cryptic lineage that is highly divergent from A. h. pondoliae farther south. Although mtDNA suggests that Umtata may represent a unique lineage sister to A. h. longiceps, mito-nuclear discordance from our RADseq data indicate that these samples may instead be closer to A. h. pondoliae, and therefore may not represent a distinct lineage. We stress the importance of recognizing that understudied populations, such as that of Umtata, may represent populations or ESUs under threat and in need of conservation attention. We present a high-quality filtered SNP dataset, comprising thousands of SNPs, which may serve as a useful resource for future golden mole studies. We have thus added to the growing body of research demonstrating the power and utility of RADseq to investigate population differentiation.
The taxonomic status and interspecies relationships of hares (genus Lepus ) in Xinjiang, China, remain ambiguous owing to extremely similar external morphologies, introgressive hybridization between species and a lack of molecular genetic records. In this study, a total of 154 hare specimens were used to clarify their taxonomic status. Based on multiple lines of evidence, including observations and comparisons of external morphological characteristics, skull morphometrics and genome‐wide single nucleotide polymorphism (SNP) datasets, four hare species were recognised. Lepus yarkandensis and Lepus timidus , which have obvious morphological characteristics, were identified as two distinct species, as previously reported. Combining the integrated morphological and molecular datasets with the relevant literature, we proposed suggestions on the classification of the more controversial hares. Due to molecular and morphological similarities, hares in northern and central Xinjiang were divided into two subspecies of Lepus tolai , namely, Lepus tolai lehmanni and Lepus tolai centrasiaticus . Despite similar external morphological characters, hares in the southwest Pamir Plateau and its surroundings can be distinguished from L. tolai by differences in skull morphology and genetic divergence and were, therefore, considered a subspecies of Lepus tibetanus , Lepus tibetanus pamirensis . Furthermore, we found that hybridization and introgression occurred between sympatric or parapatric hares, especially between L. yarkandensis and L. tibetanus pamirensis , L. yarkandensis and L. tolai centrasiaticus , and L. tolai lehmanni and L. timidus .
The broom hare (Lepus castroviejoi) is a threatened Iberian endemic, for which there is limited knowledge. We use genetic non-invasive sampling (gNIS; N = 185 faeces samples) and specimens from hunting and roadkills (N = 22) in conjunction with a 15-microsatellite panel and a 541-bp fragment of cytochrome-b to assess the genetic diversity, population structure and evolutionary history of this species. Populations from the other four European hare species were also analysed to accurately compare the genetic diversity patterns and infer admixture. Species identification from gNIS was inferred using small fragments of cytochrome-b and transferrin genes and individual identification was obtained using microsatellites. The broom hare population showed the lowest level of nuclear DNA diversity of all analysed hare species (N = 76; Na = 2.53, He = 0.186 and Fis = 0.341) and very low mitochondrial DNA diversity (N = 64; Hd = 0.743 and π = 0.01543). Only the Italian hare (L. corsicanus) showed a similar pattern of low genetic diversity. No hybridization with the neighbouring hare species was detected. However, two mitochondrial DNA lineages, corresponding to two ancient events of introgression of mountain hare (L. timidus) origin, were characterized. There was evidence for shallow spatial population differentiation of the broom hare. The described reduced genetic diversity, associated with a narrow distribution range and recent population declines, represents a risk of population extinction, and highlights the need for conservation measures of this endemic threatened hare species.
Background
Anthropogenic factors potentially affect observed biogeographical patterns in population genetics, but the effects of ancient human activities on the original patterns created by natural processes are unknown. Sinotaia quadrata , a widely distributed freshwater snail species in East Asia, was used to investigate this issue. It is unclear whether S. quadrata in Japan was introduced from China and how different human uses and varying geographic patterns affect the contemporary population genetics between the two regions. Thus, we investigated the demography of S. quadrata and detected its genetic structure in Japan and continental East Asia.
Results
Sinotaia quadrata populations first naturally migrated from continental East Asia to Japan, which is associated with the ancient period in Japanese geohistory (about 70,000 years ago). They were then artificially introduced in association with agriculture expansion by human movements in two recent periods (about 8,000 and 1,200 years ago). Populations in different parts of Japan have their own sources. Natural migration in the ancient period and artificial introduction in the recent period suggest that the population distribution is affected by both the geohistory of East Asia and the history of human expansion. In the background of the historical migration and introduction, contemporary populations in the two regions show different genetic patterns. Population divergence levels were significantly correlated with geographical patterns in Japan and significantly correlated with human interventions variables in continental East Asia, suggesting that long‐term geographical isolation is likely the major factor that shaped the contemporary population genetics in Japan, while modern human uses are likely the major factor in continental East Asia.
Conclusions
Our preliminary results show a complex demography and unusual genetic patterns in the contemporary populations for a common freshwater snail and are of significance to determine the historical formation and contemporary patterns of biogeography in Japan and continental East Asia.
A bstract
Hybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares ( Lepus ) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification of Lepus , we analyzed whole exome sequences (61.7 Mb) from 15 species of hares (1- 4 individuals per species), spanning the global distribution of the genus, and two outgroups. We used a coalescent framework to infer species relationships and divergence times, despite extensive genealogical discordance. We found high levels of allele sharing among species and show that this reflects extensive incomplete lineage sorting and temporally layered hybridization. Our results revealed recurrent introgression at all stages along the Lepus radiation, including recent gene flow between extant species since the last glacial maximum, but also pervasive ancient introgression occurring since near the origin of the hare lineages. We show that ancient hybridization between northern hemisphere species has resulted in shared variation of potential adaptive relevance to highly seasonal environments, including genes involved in circadian rhythm regulation, pigmentation, and thermoregulation. Our results illustrate how the genetic legacy of ancestral hybridization may persist across a radiation, leaving a long-lasting signature of shared genetic variation that may contribute to adaptation within and among species.
Background: The extent to which selection determines interspecific patterns of genetic exchange enlightens the role of adaptation in evolution and speciation. Often reported extensive interspecific introgression could be selection-driven, but also result from demographic processes, especially in cases of invasive species replacements, which can promote introgression at their invasion front. Because invasion and selective sweeps similarly mold variation, population genetics evidence for selection can only be gathered in an explicit demographic framework. The Iberian hare, Lepus granatensis, displays in its northern range extensive mitochondrial DNA introgression from L. timidus, an arctic/boreal species that it replaced locally after the last glacial maximum. We use whole-genome sequencing to infer geographic and genomic patterns of nuclear introgression and fit a neutral model of species replacement with hybridization, allowing us to evaluate how selection influenced introgression genome-wide, including for mtDNA.
Results:Although the average nuclear and mtDNA introgression patterns contrast strongly, they fit a single demographic model of post-glacial invasive replacement of timidus by granatensis. Outliers of elevated introgression include several genes related to immunity, spermatogenesis, and mitochondrial metabolism. Introgression is reduced on the X chromosome and in low recombining regions.
Conclusions:General nuclear and mtDNA patterns of introgression can be explained by purely demographic processes. Hybrid incompatibilities and interplay between selection and recombination locally modulate levels of nuclear introgression. Selection promoted introgression of some genes involved in conflicts, either interspecific (parasites) or possibly cytonuclear. In the latter case, nuclear introgression could mitigate the potential negative effects of alien mtDNA on mitochondrial metabolism and male-specific traits.
Hybrid camouflage variation
Snowshoe hares molt from a brown coat to a white coat in winter. In some populations, however, where winter snow is less extensive, hares molt from a brown coat to a brown coat. Jones et al. show that regulation of the pigmentation gene Agouti is responsible for the winter coat color change. Hybridization with jackrabbits has led to introgression around this gene that facilitates the brown winter morph. Hybridization appears to have provided important adaptive variation to the snowshoe hare.
Science , this issue p. 1355
The Tsugaru Strait is often referred to as Blakiston's Line in biogeography. Although this strait is thought to have become narrower during the Last Glacial Maximum (LGM), it did not close completely to form a land bridge. Sea-level drawdown associated with cooling nevertheless weakened the influence of the Tsugaru Strait as a barrier to faunal migration. The currently accepted hypothesis is that only some large and highly mobile ungulates were able to migrate to Honshu over this strait to the exclusion of small mammals. However, this remains problematic as very few fossils corroborate this idea, and quantitative identification methods for use with tiny fragments of teeth have not been developed. In this study, we determine which of the species Lepus timidus (now distributed on Hokkaido and to the north) and L. brachyurus (now mainly distributed on Honshu, Shikoku, and Kyushu) can accurately be identified within a sample of Late Pleistocene Lepus sp. fossils recently unearthed from the Shitsukari-Abe cave to the immediate south of the Tsugaru Strait. This is because we are unable to exclude the possibility that these fossils are referable to L. timidus based on site location alone. Thus, utilizing images of mandibular third premolar teeth obtained via microcomputed tomography (CT) scanning, we report (1) linear measurements, (2) a survey of the frequency of appearance of non-metric traits, and (3) principal component analysis (PCA) using landmark (LM) methods. The results show that fossil representatives of the genus Lepus can be differentiated from extant L. timidus and closely resemble L. brachyurus. Considering the past allopatric distribution of the two species suggested by other studies as well as fossil records around the Tsugaru Strait, this result corroborates the existing hypothesis that only large and highly mobile ungulates were able to navigate the Tsugaru Strait.
In Fennoscandia, mountain hare (Lepus timidus) and brown hare (Lepus europaeus) hybridize and produce fertile offspring, resulting in gene flow across the species barrier. Analyses of maternally inherited mitochondrial DNA (mtDNA) show that introgression occur frequently, but unavailability of appropriate nuclear DNA markers has made it difficult to evaluate the scale- and significance for the species. The extent of introgression has become important as the brown hare is continuously expanding its range northward, at the apparent expense of the mountain hare, raising concerns about possible competition. We report here, based on analysis of 6833 SNP markers, that the introgression is highly asymmetrical in the direction of gene flow from mountain hare to brown hare, and that the levels of nuclear gene introgression are independent of mtDNA introgression. While it is possible that brown hares obtain locally adapted alleles from the resident mountain hares, the low levels of mountain hare alleles among allopatric brown hares suggest that hybridization is driven by stochastic processes. Interspecific geneflow with the brown hare is unlikely to have major impacts on mountain hare in Fennoscandia, but direct competition may.
Aims The 50th anniversary of the publication of the seminal book, The Theory of Island Biogeography, by Robert H. MacArthur and Edward O. Wilson is a timely moment to review and identify key research foci that could advance island biology. Here, we take a collaborative horizon-scanning approach to identify 50 fundamental questions for the continued development of the field.
Location Worldwide.
Methods We adapted a well-established methodology of horizon scanning to identify priority research questions in island biology, and initiated it during the Island Biology 2016 conference held in the Azores. A multidisciplinary working group prepared an initial pool of 187 questions. A series of online surveys was
then used to refine a list of the 50 top priority questions. The final shortlist was restricted to questions with a broad conceptual scope, and which should be answerable through achievable research approaches.
Results Questions were structured around four broad and partially overlapping island topics, including: (Macro)Ecology and Biogeography, (Macro)Evolution, Community Ecology, and Conservation and Management. These topics were then subdivided according to the following subject areas: global diversity patterns (five questions in total); island ontogeny and past climate change (4); island rules and syndromes (3); island biogeography theory (4); immigration–speciation–extinction dynamics (5); speciation and diversification (4); dispersal and colonization (3); community assembly (6); biotic interactions (2); global change (5); conservation and management policies (5); and invasive alien species (4).
Main conclusions Collectively, this cross-disciplinary set of topics covering the 50 fundamental questions has the potential to stimulate and guide future research in island biology. By covering fields ranging from biogeography, community ecology and evolution to global change, this horizon scan has the potential to foster the formation of interdisciplinary research networks, enhancing joint efforts to better understand past, present and future of island biotas.
Introgressive hybridization is an important and widespread evolutionary process, but the relative roles of neutral demography and natural selection in promoting massive introgression are difficult to assess and an important matter of debate. Hares from the Iberian Peninsula provide an appropriate system to study this question. In its northern range, the Iberian hare, Lepus granatensis, shows a northwards gradient of increasing mitochondrial DNA (mtDNA) introgression from the arctic/boreal L. timidus, which it presumably replaced after the last glacial maximum. Here, we asked whether a south-north expansion wave of L. granatensis into L. timidus territory could underlie mtDNA introgression, and whether nuclear genes interacting with mitochondria (“mitonuc” genes) were affected. We extended previous RNA-sequencing and produced a comprehensive annotated transcriptome assembly for L. granatensis. We then genotyped 100 discovered nuclear SNPs in 317 specimens spanning the species range. The distribution of allele frequencies across populations suggests a northwards range expansion, particularly in the region of mtDNA introgression. We found no correlation between variants at 39 mitonuc genes and mtDNA introgression frequency. Whether the nuclear and mitochondrial genomes coevolved will need a thorough investigation of the hundreds of mitonuc genes, but range expansion and species replacement likely promoted massive mtDNA introgression.
The taxonomic status of the species Lepus melainus, the Manchurian black hare, is intensely debated. It is considered either as a valid species or a black color morph of L. mandshuricus, the Manchurian hare. Herein, we evaluate the validity of L. melainususing 24 morphological traits and two nuclear DNA loci (TG=466bp; MGF=592bp) from newly collected specimens. Except for winter pelage, we fail to discover significant morphological differences between L. melainus and L. mandshuricus. Analysis of the nuclear DNA sequences reveals lack of reciprocal monophyly between L. mandshuricus and L. melainus, as they form one single clade with high bootstrap support; in addition, morphometric and morphological analyses found no specific differentiation between forms corresponding to L. mandshuricus or L. melainus. Together with the fact that the range of L. melainus is completely within that of L. mandshuricus, our study supports the recognition of L. melainus as a melanistic morph and junior synonym of L. mandshuricus.
The study of islands as model systems has played an important role in the development of evolutionary and ecological theory. The 50th anniversary of MacArthur and Wilson's (December 1963) article, ‘An equilibrium theory of insular zoogeography’, was a recent milestone for this theme. Since 1963, island systems have provided new insights into the formation of ecological communities. Here, building on such developments, we highlight prospects for research on islands to improve our understanding of the ecology and evolution of communities in general. Throughout, we emphasise how attributes of islands combine to provide unusual research opportunities, the implications of which stretch far beyond islands. Molecular tools and increasing data acquisition now permit re-assessment of some fundamental issues that interested MacArthur and Wilson. These include the formation of ecological networks, species abundance distributions, and the contribution of evolution to community assembly. We also extend our prospects to other fields of ecology and evolution – understanding ecosystem functioning, speciation and diversification – frequently employing assets of oceanic islands in inferring the geographic area within which evolution has occurred, and potential barriers to gene flow. Although island-based theory is continually being enriched, incorporating non-equilibrium dynamics is identified as a major challenge for the future.
Hybridization drives the evolutionary trajectory of many species or local populations, and assessing the geographic extent and genetic impact of interspecific gene flow may provide invaluable clues to understand population divergence or the adaptive relevance of admixture. In North America, hares (Lepus spp.) are key species for ecosystem dynamics and their evolutionary history may have been affected by hybridization. Here we reconstructed the speciation history of the three most widespread hares in North America - the snowshoe hare (Lepus americanus), the white-tailed jackrabbit (L. townsendii) and the black-tailed jackrabbit (L. californicus) - by analyzing sequence variation at eight nuclear markers and one mitochondrial DNA (mtDNA) locus (6 240 bp; 94 specimens). A multilocus-multispecies coalescent-based phylogeny suggests that L. americanus diverged ~2.7 Mya and that L. californicus and L. townsendii split more recently (~1.2 Mya). Within L. americanus a deep history of cryptic divergence (~2.0 Mya) was inferred, which coincides with major speciation events in other North American species. While the isolation-with-migration model suggested that nuclear gene flow was generally rare or absent among species or major genetic groups, coalescent simulations of mtDNA divergence revealed historical mtDNA introgression from L. californicus into the Pacific Northwest populations of L. americanus. This finding marks a history of past reticulation between these species, which may have affected other parts of the genome and influence the adaptive potential of hares during climate change.This article is protected by copyright. All rights reserved.
Ursine bears are a mammalian subfamily that comprises six morphologically and ecologically distinct extant species. Previous phylogenetic analyses of concatenated nuclear genes could not resolve all relationships among bears, and appeared to conflict with the mitochondrial phylogeny. Evolutionary processes like incomplete lineage sorting and introgression can cause gene tree discordance and complicate phylogenetic inferences, but are not accounted for in phylogenetic analyses of concatenated data. We generated a high-resolution data set of autosomal introns from several individuals per species and of Y-chromosomal markers. Incorporating intraspecific variability in coalescence-based phylogenetic and gene flow estimation approaches, we traced the genealogical history of individual alleles. Considerable heterogeneity among nuclear loci and discordance between nuclear and mitochondrial phylogenies were found. A species tree with divergence time estimates indicated that ursine bears diversified within less than two million years. Consistent with a complex branching order within a clade of Asian bear species, we identified unidirectional gene flow from Asian black into sloth bears. Moreover, gene flow detected from brown into American black bears can explain the conflicting placement of the American black bear in mitochondrial and nuclear phylogenies. These results highlight that both incomplete lineage sorting and introgression are prominent evolutionary forces even on time scales up to several million years. Complex evolutionary patterns are not adequately captured by strictly bifurcating models, and can only be fully understood when analyzing multiple independently inherited loci in a coalescence framework. Phylogenetic incongruence among gene trees hence needs to be recognized as a biologically meaningful signal.
The 21st century is projected to witness unprecedented climatic changes, with greater warming often reported for high latitudes.
Yet, climate change can be measured in a variety of ways, reflecting distinct dimensions of change with unequal spatial patterns
across the world. Polar climates are projected to not only warm, but also to shrink in area. By contrast, today’s hot and
arid climates are expected to expand worldwide and to reach climate states with no current analog. Although rarely appreciated
in combination, these multiple dimensions of change convey complementary information. We review existing climate change metrics
and discuss how they relate to threats and opportunities for biodiversity. Interpreting climate change metrics is particularly
useful for unknown or poorly described species, which represent most of Earth’s biodiversity.
We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular BEAST 1 platform to correct structural deficiencies that became evident as the BEAST 1 software evolved. Key among those deficiencies was the lack of post-deployment extensibility. BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform. This package architecture is showcased with a number of recently published new models encompassing birth-death-sampling tree priors, phylodynamics and model averaging for substitution models and site partitioning. A second major improvement is the ability to read/write the entire state of the MCMC chain to/from disk allowing it to be easily shared between multiple instances of the BEAST software. This facilitates checkpointing and better support for multi-processor and high-end computing extensions. Finally, the functionality in new packages can be easily added to the user interface (BEAUti 2) by a simple XML template-based mechanism because BEAST 2 has been re-designed to provide greater integration between the analysis engine and the user interface so that, for example BEAST and BEAUti use exactly the same XML file format.
Mitochondria play a fundamental role in cellular metabolism, being responsible for most of the energy production of the cell in the oxidative phosphorylation (OXPHOS) pathway. Mitochondrial DNA (mtDNA) encodes for key components of this process but its direct role in adaptation remains far from understood. Hares (Lepus spp.) are privileged models to study the impact of natural selection on mitogenomic evolution because i) species are adapted to contrasting environments, including arctic, with different metabolic pressures, and ii) mtDNA introgression from arctic into temperate species is widespread. Here, we analyzed the sequences of 11 complete mitogenomes (10 newly obtained) of hares of temperate and arctic origins (including two of arctic origin introgressed into temperate species). The analysis of patterns of codon substitutions along the reconstructed phylogeny showed evidence for positive selection in several codons in genes of the OXPHOS complexes, most notably affecting the arctic lineage. However, using theoretical models, no predictable effect of these differences was found on the structure and physicochemical properties of the encoded proteins, suggesting that the focus of selection may lie on complex interactions with nuclear encoded peptides or on amino acid composition. Also, a cloverleaf structure was detected in the control region only from the arctic mtDNA lineage, which may influence mtDNA replication and transcription. These results suggest that adaptation impacted the evolution of hare mtDNA and may have influenced the occurrence and consequences of the many reported cases of massive mtDNA introgression. However the origin of adaptation remains elusive.
The evolution of the mitochondrial genome and its potential adaptive impact still generates vital debates. Even if mitochondria have a crucial functional role, as they are the main cellular energy suppliers, mitochondrial DNA (mtDNA) introgression is common in nature, introducing variation in populations upon which selection may act. Here we evaluated whether the evolution of mtDNA in a rodent species affected by mtDNA introgression is explained by neutral expectations alone. Variation in one mitochondrial and six nuclear markers in Myodes glareolus voles was examined, including populations that show mtDNA introgression from its close relative, Myodes rutilus. In addition, we modelled protein structures of the mtDNA marker (cytochrome b) and estimated the environmental envelopes of mitotypes. We found that massive mtDNA introgression occurred without any trace of introgression in the analysed nuclear genes. The results show that the native glareolus mtDNA evolved under past positive selection, suggesting that mtDNA in this system has selective relevance. The environmental models indicate that the rutilus mitotype inhabits colder and drier habitats than the glareolus one that can result from local adaptation or from the geographic context of introgression. Finally, homology models of the cytochrome b protein revealed a substitution in rutilus mtDNA in the vicinity of the catalytic fraction, suggesting that differences between mitotypes may result in functional changes. These results suggest that the evolution of mtDNA in Myodes may have functional, ecological and adaptive significance. This work opens perspective onto future experimental tests of the role of natural selection in mtDNA introgression in this system.Heredity advance online publication, 2 April 2014; doi:10.1038/hdy.2014.28.
We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements our RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.
Recent genetic studies have shown that introgression rates among loci may greatly vary according to their location in the genome. In particular, several cases of mito-nuclear discordances have been reported for a wide range of organisms. In the present study, we examine the causes of discordance between mitochondrial (mtDNA) and nuclear DNA introgression detected in North American populations of the Great Black-backed Gull (Larus marinus), a Holarctic species, from the Nearctic North American Herring Gull (Larus smithsonianus). Our results show that extensive unidirectional mtDNA introgression from Larus smithsonianus into Larus marinus in North America cannot be explained by ancestral polymorphism but most likely results from ancient hybridization events occurring when Larus marinus invaded the North America. Conversely, our nuclear DNA results based on 12 microsatellites detected very little introgression from Larus smithsonianus into North American Larus marinus. We discuss these results in the framework of demographic and selective mechanisms that have been postulated to explain mito-nuclear discrepancies. We were unable to demonstrate selection as the main cause of mito-nuclear introgression discordance but cannot dismiss the possible role of selection in the observed pattern. Among demographic explanations, only drift in small populations and bias in mate choice in an invasive context may explain our results. As it is often difficult to demonstrate that selection may be the main factor driving the introgression of mitochondrial DNA in natural populations, we advocate that evaluating alternative demographic neutral hypotheses may help to indirectly support or reject hypotheses invoking selective processes.Heredity advance online publication, 9 October 2013; doi:10.1038/hdy.2013.98.
Gene flow among populations or species and incomplete lineage sorting (ILS) are two evolutionary processes responsible for generating gene tree discordance and therefore hindering species tree estimation. Numerous studies have evaluated the impacts of ILS on species tree inference, yet the ramifications of gene flow on species trees remain less studied. Here, we simulate and analyze multilocus sequence data generated with ILS and gene flow to quantify their impacts on species tree inference. We characterize species tree estimation errors under various models of gene flow, such as the isolation-migration model, the n-island model, and gene flow between non-sister species or involving ancestral species, and species boundaries crossed by a single gene copy (allelic introgression) or by a single migrant individual. These patterns of gene flow are explored on species trees of different sizes (4 vs. 10 species), at different time scales (shallow vs. deep), and with different migration rates. Species trees are estimated with the multispecies coalescent model using Bayesian methods (BEST and *BEAST) and with a summary statistic approach (MPEST) that facilitates phylogenomic-scale analysis. Even in cases where the topology of the species tree is estimated with high accuracy, we find that gene flow can result in overestimates of population sizes (species tree dilation) and underestimates of species divergence times (species tree compression). Signatures of migration events remain present in the distribution of coalescent times for gene trees, and with sufficient data it is possible to identify those loci that have crossed species boundaries. These results highlight the need for careful sampling design in phylogeographic and species delimitation studies as gene flow, introgression, or incorrect sample assignments can bias the estimation of the species tree topology and of parameter estimates such as population sizes and divergence times.
Hybridization and introgression have important consequences in evolution, such as increasing the genetic diversity and adaptive potential of a species. One of their most conspicuous footprints is discordance among gene trees or between genes and phenotypes. However, most studies that report introgression fail to disprove the null hypothesis that genetic incongruence may result from stochastic sorting of ancestral allelic polymorphisms. In the case of ancient introgression, these two processes may be especially difficult to distinguish topologically, but they make different predictions about the patterns of coalescence among loci. Here we apply three methods, molecular dating, multispecies coalescent models, and gene tree simulation under coalescence, to compare these two hypotheses that explain the polyphyletic mtDNA of the butterfly peacock bass, Cichla orinocensis. In comparison with a species tree based on 20 unlinked nuclear loci, we determined that mtDNA divergences were too recent to be explained by ancestral polymorphism. Similarly, coalescent species tree branches were significantly shorter when putative introgressed mtDNA was incorporated, and simulations showed the mtDNA topology to be unlikely under lineage sorting only. We conclude that introgression approximately 1.5 million years ago resulted in capture by C. orinocensis of an mtDNA lineage ancestral to the modern subspecies C. oc. monoculus.
Melanism is a common phenomenon in the animal kingdom. While the occurrence of melanism in lagomorphs has been less studied, this phenomenon has led to systematic confusion among different forms of pikas (Ochotona) and hares (Lepus). Within Ochotona, the Pianma black pika (O. nigritia) was established primarily based on its pelage phenotype variation compared with the sympatric Forrest's pika (O. forresti). The Gaoligong pika (O. gaoligongensis) was also described based on pelage color differences with O. forresti. However, the specific status of these two taxa has been questioned for several years. We conducted a detailed examination of the cranial characters used for the initial diagnosis of each of these forms (O. forresti, O. gaoligongensis and O. nigritia). Insignificant differences were displayed among these species, thus contradicting the classification of O. gaoligongensis and O. nigritia as separate species. Within Lepus, the Manchurian black hare (Lepus melainus) was also initially described based on the melanistic pelage possessed by this form. We conducted a detailed examination of the cranial characteristics of L. melainus and the sympatric Manchurian hare (L. mandshuricus) and confirmed the synonomy of these forms; L. melainus represents melanistic individuals of L. mandshuricus. These taxonomic mistakes probably resulted from underestimating the prevalence of melanism and the potential for adaptative variation of pelage coloration in nature. A more detailed study on the genetic background leading to the occurrence of melanistic lagomorphs is needed.
In the Quaternary, the Ryukyu Islands evolved from a continental margin arc to an island arc by backarc spreading of the Okinawa Trough, accompanied by subsidence and isolation of the islands, a process that has continued to the present. Trough-parallel half grabens were filled with marine siltstone. Similar sediments filling orthogonal fault-controlled and west-draining non-tectonic valleys record island separation. New Quaternary nannofossil biostratigraphic data date the deposition of the marine siltstone at 1.552 ± 0.154 Ma. At that time, the entire 1000 km-long island chain comprising the Ryukyu Islands separated from the Asian continent by rifting extending from the Okinawa Trough to the Tsushima Strait. The Tokara, Kerama, and Yonaguni gaps, branched or transverse rifts of the Okinawa Trough, separate the island chain into subgroups of the Osumi, Amami, Okinawa, and Yaeyama islands, and Taiwan. The shallow Taiwan Strait separated Taiwan from the Chinese mainland. The Kuroshio warm current that previously ran offshore of the continental margin arc began to enter the opening backarc basin through the Yonaguni gap and to exit through the Tokara gap, flowing along the axis of the Okinawa Trough. Under influence of the warm current and because of entrapment of continentally sourced detrital sediments by the Okinawa Trough, coral reefs formed around each island. These reefs make up a unit called the Ryukyu limestone. Subsidence continued through the deposition of this limestone, resulting in further isolation of each island. Some islands did not separate from the mainland but emerged above sea level later as a result of volcanic edifice construction or forearc uplift. Following initial isolation, the Japanese islands and Taiwan may have been connected to the mainland by land bridges during some sea level low stands related to glacial periods, whereas the other islands remained isolated. Based on ages of isolation of each island, a Quaternary palaeogeographic map and ‘phylogenetic tree’ of the islands can be drawn showing the separation time of each island from the mainland and from each other. This information should be useful for phylogenetic molecular biologists studying evolution of Ryukyu endemic species and vicariant speciation and could facilitate analysis of the DNA substitution rate.
We assessed dispersal and vicariant events in four species of Japanese moles in the genera Mogera and Euroscaptor to better understand the factors shaping intra- and interspecific differentiation in Japanese moles. We used the combined viewpoints of molecular phylogeny and historical geology using nucleotide sequences of mitochondrial (cytochrome b; Cytb) and nuclear (A2ab, Bmp4, Tcf25, vWf) genes. The divergence times estimated from the molecular data were verified with available geological data on the chronology of fluctuations in sea level in the Korea Strait, assuming sequential migration and speciation events. This produced possible migration times of 5.6, 3.5, 2.4, and 1.3 million years ago for four species of Japanese moles, Euroscaptor mizura, Mogera tokudae, M. imaizumii, and M. wogura, respectively. For the western Japanese mole M. wogura, Cytb sequences revealed four major phylogroups with strong geographic affinities in southwestern Central Honshu (I), western Honshu/Shikoku (II), Kyushu/westernmost Honshu (III), and Korea/Russian Primorye (IV). The nuclear gene sequences supported the distinctiveness of phylogroups I and IV, indicating long, independent evolutionary histories. In contrast, phylogroups II and III were merged into a single geographic group based on the nuclear gene data. Intraspecific divergences in M. imaizumii and M. tokudae were rather apparent in Cytb but not in nuclear gene sequences. The results suggest that repeated dispersal events have occurred between the Asian continent and the Japanese Islands, and intensive vicariant events associated with abiotic and biotic factors have created higher levels of species and genetic diversities in moles occurring on the Japanese Islands.
Hybridization has many and varied impacts on the process of speciation. Hybridization may slow or reverse differentiation by allowing gene flow and recombination. It may accelerate speciation via adaptive introgression or cause near-instantaneous speciation by allopolyploidization. It may have multiple effects at different stages and in different spatial contexts within a single speciation event. We offer a perspective on the context and evolutionary significance of hybridization during speciation, highlighting issues of current interest and debate. In secondary contact zones, it is uncertain if barriers to gene flow will be strengthened or broken down due to recombination and gene flow. Theory and empirical evidence suggest the latter is more likely, except within and around strongly selected genomic regions. Hybridization may contribute to speciation through the formation of new hybrid taxa, whereas introgression of a few loci may promote adaptive divergence and so facilitate speciation. Gene regulatory networks, epigenetic effects and the evolution of selfish genetic material in the genome suggest that the Dobzhansky–Muller model of hybrid incompatibilities requires a broader interpretation. Finally, although the incidence of reinforcement remains uncertain, this and other interactions in areas of sympatry may have knock-on effects on speciation both within and outside regions of hybridization.
We examined the phylogenetic status and history of the mountain hare Lepus timidus in and around Hokkaido using mitochondrial cytochrome b (cyt b) sequences from 158 samples from Hokkaido and 14 from Sakhalin, as well as four samples from the Korean hare, L. coreanus. The phylogenetic analysis of the cyt b sequences generated in this study and obtained from DNA databases showed the clear genetic specificity of the Hokkaido lineage as a clade. The Hokkaido lineage was estimated to have diverged from the other conspecific and L. coreanus lineages 0.46 and 0.30 million years ago (Mya), respectively. These results suggest that the common ancestor of the mitochondrial lineage in Hokkaido and Korea inhabited Far East Asia before colonization by the present continental lineages of L. timidus, including the Sakhalin population. We estimated the time of the most recent common ancestor of the Hokkaido population to be 0.17 Mya, and found two distinct haplogroups within the island. One group had greater genetic diversity (mean number of pairwise differences: π = 0.0188 ± 0.0108) and appears to have expanded from the west to the entire island of Hokkaido. The other had lower genetic diversity (π = 0.0038 ± 0.0037) and its distribution was concentrated in the east. These contrasting west/east trends indicate that the Hokkaido population was fragmented in the past, and then subsequently expanded. Our study suggests that Hokkaido was an important refugium for boreal species in the far eastern region, and allowed the formation of various population genetic structures within the island.
The phylogeography of four Apodemus species (Apodemus agrarius, Apodemus peninsulae, Apodemus latronum, and Apodemus draco) was studied in the Far East of Asia, based on sequences of the mitochondrial DNA cytochrome b gene. The results obtained show the existence of many different genetic lineages within the studied Apodemus species, suggesting the isolation and differentiation of populations in multiple refuge areas. Higher genetic diversities in some regions such as Yunnan, Sichuan (China), and eastern Russia suggest these areas are potential refuges for these species. The existence of such complex genetic structures could be linked to the presence of many biogeographic barriers (Himalaya Mountains, Tien-shan Mountains, Altai Mountains, Tibetan Plateau, Gobi desert, Yunnan Guizhou Plateau, Dzungaria basin, and others) in these regions, which were probably reinforced during the Quaternary climate changes. These barriers also played an important role concerning the low dispersal abilities of the two studied Apodemus species adapted to forest habitats (A. latronum and A. draco) with respect to colonizing regions other than China.
In studies of phylogeography and taxonomy, strong emphasis is usually placed on the study of mitochondrial (mt)DNA. In the present study, we present a remarkable case in which highly phenotypically divergent species have almost no divergence in mtDNA. Yellowhammers (Emberiza citrinella Linnaeus) and pine buntings (Emberiza leucocephalos S. G. Gmelin) differ noticeably in appearance and song but hybridize in some areas of contact. They share a variety of closely-related mtDNA haplotypes, with little divergence in frequencies, indicating a mitochondrial divergence time sometime during or after the last major glacial period. By contrast, nuclear DNA (amplified fragment length polymorphism markers and CHD1Z gene sequences) differs more strongly between the species, and these differences can be used to identify intermediate genetic signatures of hybrids. The combined amount of mitochondrial diversity within yellowhammers and pine buntings is very low compared to other Emberiza species pairs, whereas the level of variation at the nuclear gene CHD1Z is comparable to that within other species pairs. Although it is difficult to completely reject the possibility that the two species split extremely recently and experienced rapid nuclear and phenotypic differentiation, we argue that the evidence better supports another possibility: the two species are older and mtDNA has recently introgressed between them, most likely as a result of a selective sweep. Mismatches between mitochondrial and nuclear phylogeographic patterns may occur more commonly than previously considered, and could have important implications for the fields of phylogeography and taxonomy. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 422–438.
Aim
The distribution of hares (Lepus spp.) in southern Europe was markedly different at the Last Glacial Maximum. Historical hybridization during range replacements led to high frequencies of mtDNA introgression from Lepus timidus into populations of three other species in northern Iberian Peninsula, even though L. timidus subsequently disappeared from the region. We use palaeontological records to provide new insights on the biogeographic history of these range replacements, combining ancient DNA and ecological niche modelling.
Location
Southern France.
Taxon
Hares (genus Lepus).
Methods
DNA was extracted from hare bones collected at Neolithic sites in southern France (5.5–7.5 thousand years before present; kyr bp) with uncertain species assignment. One mtDNA fragment was sequenced and 27 SNPs from 11 nuclear genes with species‐diagnostic information were genotyped. Distributions of L. granatensis, L. europaeus, and L. timidus were modelled using spatial and bioclimatic predictors, and the favourability function. Each model was transferred to 6 kyr bp and favourabilities were combined to determine the species with the highest environmental favourability in each sampled locality.
Results
Ancient DNA analysis showed that the screened specimens belong to L. granatensis, a species presently confined to the Iberian Peninsula, but carried mtDNA haplotypes from L. timidus. Niche models show that L. granatensis achieved highest favourability in southern France 6 kyr bp reinforcing the molecular evidences.
Main conclusions
L. granatensis replaced L. timidus populations from Iberia to southern France, being present in this region 5.5 kyr bp. Subsequent westwards invasion of L. europaeus likely replaced these L. granatensis populations towards northern Iberia, establishing current ranges. Despite successive species replacements, introgressed mtDNA haplotypes from L. timidus mark the distribution of the species in northern Iberian Peninsula before it disappeared in the region. Characterizing complex biogeographic histories of interacting species is a key to understand processes that led to current distributions of genetic diversity.
The circum-Japan Sea region (CJSR) greatly impacted animal diversity in the Eastern Palearctic during the Quaternary. However, its role in avian diversification has been underestimated because of the high dispersal capabilities of birds over the sea. We investigated the phylogeographic and demographic history of the Eurasian Jay (Garrulus glandarius), focusing on CJSR populations. We sequenced a total of 1744 bp of mitochondrial DNA (cytochrome b and control region) from 73 samples. Together with the database sequences, we reconstructed a phylogenetic tree for the Eurasian Jay over the Palearctic. The earliest phylogenetic divergence was inferred to be related to geological vicariance between the Japanese archipelago and Eurasian mainland around the Pliocene–Pleistocene boundary. Several demographic analyses have suggested that there are two divergent subspecies across the CJSR, G. g. brandtii on the mainland, Sakhalin, and Hokkaido and G. g. japonicus in the archipelago. These simultaneously experienced population contractions to independent refugia and subsequent expansions around the last glacial period, i.e., parallel population dynamics. We suggest that the two landmasses of the CJSR were important for generating and preserving the phylogenetic structure of the Eurasian Jay.
Climate change enables expansion of southern species whereas many boreal species retreat northwards. Range shifts create novel interactions that can affect abundance and distribution via competition and/or hybridization. It is possible that the mountain hare (Lepus timidus) long-term decline in northern Europe is linked to competition with the brown hare (L. europaeus). In order to understand consequences of hare interactions at high latitudes, we determined geographical extent of hybridization using mitochondrial DNA (mtDNA) introgression as a proxy. Additionally, we compared species distribution and snow conditions in Finland with introgression frequency. We found that introgression is bidirectional but direction is mostly from the mountain hare to the brown hare. Approximately 10% of brown hares have introgressed mtDNA, being most common at the northern expansion front of their distribution range. Introgression is likely linked to brown hare expansion facilitated by climate change, but due to complex nature of evolutionary processes, selective advantage cannot be fully excluded.
Full text at: http://www.sekj.org/PDF/anz55-free/anz55-015-024-free.pdf
Reliable estimates of evolutionary rates of mitochondrial DNA might allow us to build realistic evo- lutionary scenarios covering broad time scales based on phylogenetic inferences. In the present study, we sought to obtain estimates of evolutionary rates in murine rodents using calibrations against historical biogeographic events. We first assumed that land-bridge-like structures that appeared intermittently at glacial maxima with 100,000-year intervals shaped the divergence pat- terns of cytochrome b (Cytb) sequences (1140 bp) of the larger Japanese wood mouse Apodemus speciosus. The comparison of sequences from peripheral remote islands that are separated from one another by deep straits allowed us to estimate mitochondrial DNA evolutionary rates (substitu- tions/site/million years) to be 0.027 to 0.036, with presumed calibrations from 140,000, 250,000, 350,000, and 440,000 years ago. Second, we addressed rapid expansion events inferred from anal- yses of the Cytb sequences of the lesser Japanese wood mouse A. argenteus. We detected five expansion signals in the dataset and established three categories based on the expansion param- eter tau values: 3.9, 5.6–5.7, and 7.8–8.1. Considering that the climate became warmer 15,000, 53,000, and 115,000 years ago after preceding periods of rapid cooling, we calculated evolutionary rates to be 0.114, 0.047, and 0.031, respectively. This preliminary concept of the evolutionary rates on a time scale from 15,000 to 440,000 years ago for the wood mouse should be refined and tested in other species of murine rodents, including mice and rats.
The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
To elucidate the origins of the Japanese mammalian fauna from the perspectives of biogeography and community ecology, I reviewed molecular phylogenetic and phylogeographic studies for all non-volant terrestrial mammals indigenous to the Japanese Archipelago (63 species), with a particular focus on obtaining reliable chronological data. The results of this review demonstrate that geological vicariance events in the Tsugaru and Korea (Tsushima) Straits can explain the distribution of many Japanese mammals, in particular the Hokkaido-endemic species with Late Pleistocene origins and the Honshu–Shikoku–Kyushu-endemic species with Middle Pleistocene or earlier origins. Phylogenetic relatedness also contributed to the observed patterns of distribution through the processes of competitive exclusion and species assortment, and abiotic environmental filtering was another important factor. Later colonists of Honshu–Shikoku–Kyushu, from northern Hokkaido or the southern Tsushima Islands, were mostly excluded owing to the competitive dominance of earlier residents or environmental filtering. On the other hand, the fragmented distributions of some species with more ancient origins in both Hokkaido and Honshu–Shikoku–Kyushu may be a result of the competitive dominance of later migrants. Ecological coexistence can be achieved by phylogenetically dispersed species, supporting the principle of species assortment. Because almost all aspects of the mammalian faunal assembly in Japan can be explained by geological events or community ecological processes, the Japanese Archipelago may be an ideal model island system in which to study the mechanisms of faunal assembly.
AimA striking case of mitochondrial DNA (mtDNA) introgression occurs in the Iberian Peninsula: the mtDNA of Lepus timidus, a species that inhabited this territory during the Last Glacial Maximum (LGM), is almost fixed in the Iberian range of Lepus europaeus, is very frequent in the northern half of Iberia within Lepus granatensis, and is fixed in Lepus castroviejoi. Here, we used a transdisciplinary approach to understand the ecological drivers of the distribution of this introgressed mtDNA in the Iberian hare species.LocationEurope, with an emphasis on the Iberian Peninsula.Methods
First, we modelled the climatic niche of L. timidus to predict the favourability for the species during the LGM. Second, we gathered data regarding L. timidus mtDNA introgression for 1137 individuals (139 populations) from the Iberian Peninsula. We tested whether the climatic favourability for L. timidus during the LGM reflects the frequency of the introgressed mtDNA in the carrier hare populations.ResultsThe climatic favourability for the LGM is positively related to the presence of individuals with L. timidus mtDNA, and discriminates better than by chance between individuals with and without this lineage. At the population level, the favourability values relate to the observed frequencies of mtDNA introgression and discriminate between populations with and without L. timidus mtDNA.Main conclusionsThe results suggest that the geographical distribution of L. timidus mtDNA introgression is linked to L. timidus distribution in Iberia during the LGM. Our study helps to improve our understanding of the role of climate in the reticulated evolutionary history of hares, and is a first step towards understanding the ecological impact of mtDNA introgression on Iberian hares.
The idea that species boundaries can be semipermeable to gene flow is now widely accepted but the evolutionary importance of introgressive hybridization remains unclear. Here we examine the genomic contribution of gene flow between two hybridizing chipmunk species, Tamias ruficaudus and Tamias amoenus. Previous studies have shown that ancient hybridization has resulted in complete fixation of introgressed T. ruficaudus mitochondrial DNA (mtDNA) in some populations of T. amoenus, but the extent of nuclear introgression is not known. We used targeted capture to sequence over 10500 gene regions from multiple individuals of both species. We found that most of the nuclear genome is sorted between these species and that overall genealogical patterns do not show evidence for introgression. Our analysis rules out all but very minor levels of interspecific gene flow, indicating that introgressive hybridization has had little impact on the overall genetic composition of these species outside of the mitochondrial genome. Given that much of the evidence for introgression in animals has come from mtDNA, our results underscore that unraveling the importance introgressive hybridization during animal speciation will require a genome-wide perspective that is still absent for many species. This article is protected by copyright. All rights reserved.
This article is protected by copyright. All rights reserved.
We examined the nucleotide sequences of the mitochondrial NADH dehydrogenase subunit 2 gene (976 base pairs) for 279 individuals of the sable Martes zibellina (Carnivora, Mustelidae), derived from diverse areas throughout the regions of the Ural Mountains to the Russian Far East on the Eurasian continent and the peripheral peninsula (Kamchatka) and islands (Sakhalin, Hokkaido, and southern Kurils). The demographic history of the sable and its migration history to the eastern peripheral peninsula and islands were inferred using phylogeographic approaches. The analyses confirmed the previously found major lineages for the examined sables and further identified novel sublineages. Our data also support that a lineage, which is endemic to the eastern marginal islands (Sakhalin, Hokkaido, and southern Kurils), was produced by the demographic expansion of an ancestral lineage in the Eurasian continent. The most recent common ancestor of the Sakhalin, Hokkaido, and southern Kuril sables was estimated to exist during the Late Pleistocene. We also determined that another lineage exists on Sakhalin and is shared by the Far East Primorsky population. Our results indicate multiple migration events onto Sakhalin from the continent and suggest the importance of the formation of several straits to the distribution of sable lineages. Meanwhile, Kamchatka is dominated by a sole lineage which would also have followed the demographic expansion on the Eurasian continent. The Russian Far East was indicated as the source area for lineage diversifications; in this region, genetic diversity was relatively high, which is consistent with previous studies.
Seasonal changes in fur colour in some mammalian species have long attracted the attention of biologists, especially in species showing population variation in these seasonal changes. Genetic differences among populations that show differences in seasonal changes in coat colour have been poorly studied. Because the Japanese hare (Lepus brachyurus) has two allopatric morphotypes that show remarkably different coat colours in winter, we examined the population genetic structure of the species using partial sequences of the SRY gene and six autosomal genes: three coat colour-related genes (ASIP, TYR, and MC1R) and three putatively neutral genes (TSHB, APOB, and SPTBN1). The phylogenetic tree of SRY sequences exhibited two distinct lineages that diverged approsimately 1 Mya. Although the two lineages exhibited a clear allopatric distribution, it was not consistent with the distribution of morphotypes. In addition, six nuclear gene sequences failed to reveal genetic differences between morphotypes. Population network trees for 11 expedient populations divided the populations into four groups. Genetic structure analysis revealed an admixture of four genetic clusters in L. brachyurus, two of which showed large genetic differences. Our results suggest ancient vicariance in L. brachyurus, and we detected no genetic differences between the two morphotypes. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, ●●, ●●–●●.
Discordance between mitochondrial and nuclear DNA has been noted in many systems. Asymmetric introgression of mitochondria is a common cause of such discordances, although in most cases the drivers of introgression are unknown. In the yellow-rumped warbler, evidence suggests that mtDNA from the eastern, myrtle warbler, has introgressed across much of the range of the western form, the Audubon's warbler. Within the southwestern United States myrtle mtDNA comes into contact with another clade that occurs in the Mexican black-fronted warbler. Both northern forms exhibit seasonal migration, whereas black-fronted warblers are nonmigratory. We investigated the link between mitochondrial introgression, mitochondrial function, and migration using novel genetic, isotopic, biochemical, and phenotypic data obtained from populations in the transition zone. Isotopes suggest the zone is coincident with a shift in migration, with individuals in the south being resident and populations further north becoming increasingly more migratory. Mitochondrial respiration in flight muscles demonstrates that myrtle-type individuals have a significantly greater acceptor control ratio of mitochondria, suggesting it may be more metabolically efficient. To our knowledge this is the first time this type of intraspecific variation in mitochondrial respiration has been measured in wild birds and we discuss how such mitochondrial adaptations may have facilitated introgression.
This paper concisely describes the land mammal faunas of the last glacial period and Holocene separately for the three biogeographic regions comprising the Japanese Islands (Hokkaido, Honshu-Shikoku-Kyushu and the Ryukyu Islands). It also outlines the extinctions and immigration of land mammals during the periods. In Hokkaido, the fauna of the last glacial period is represented only by a few extinct large mammal species. It is inferred that the Mammoth Fauna immigrated from eastern Siberia into Hokkaido during this period. The large mammal species of the last glacial period became extinct possibly by the beginning of the Holocene. The Holocene fauna of Hokkaido is almost idenfical with its present-day fauna, and no mammals immigrated into Hokkaido during the Holocene. In Honshu-Shikoku-Kyushu, the last glacial fauna is predominated by extant species now distributed in this region, and contains several extinct species as well as several extant species now exotic to this region. The extinct and exotic species seem to have become extinct between ca. 20,000 and ca. 10,000yrsBP in radiocarbon age. During the last glacial period, few elements of the Mammoth Fauna immigrated into Honshu-Shikoku-Kyushu from Hokkaido. Such limited immigration is inferred to have occurred through temporary ice bridges formed across the Tsugaru Stait instead of a stable land bridge. In Honshu-Shikoku-Kyushu, the Holocene fauna is almost identical with the present-day fauna, and no mammals immigrated into this region during the Holocene. In the Ryukyu Islands, the last glacial fauna is of insular type, and its main elements including middle- and small-sized deer became extinct possibly by the beginning of the Holocene. No mammals immigrated into the Ryukyu Islands during the last glacial period and Holocene.
Many Japanese geologists estimate -100 to -140 m for the last glacial low stand sea level, but some doubt is cast on their data and opinions. Our estimate of -80 ± 5 m was a conservative interpretation based on dates for shells and peat obtained from the shelf and coastal plains of the Japanese Islands. For most of the Pleistocene, the Japanese Islands were connected with the Korean Peninsula, and the present major islands themselves were tied to each other. Large mammals such as elephants migrated into the Japanese Islands through land bridges. In the early Shimosueyoshi transgression (about 100 000 y BP), when the sea level was about -100 m, the Japan Sea was connected with the Pacific through narrow passages located in the Korean and Tsugaru straits. -from English summary
I analyze a number of widespread misconceptions concerning species. The species category, defined by a concept, denotes the rank of a species taxon in the Linnaean hierarchy. Biological species are reproducing isolated from each other, which protects the integrity of their genotypes. Degree of morphological difference is not an appropriate species definition. Unequal rates of evolution of different characters and lack of information on the mating potential of isolated populations are the major difficulties in the demarcation of species taxa.
This work uses an atmospheric general circulation model (AGCM) asynchronously coupled to an equilibrium vegetation model to investigate whether vegetation feedbacks could be one of the reasons why the Late Saalian ice sheet (140 kyrs BP) in Eurasia was substantially larger than the Last Glacial Maximum (LGM, 21 kyrs BP) Eurasian ice sheet. The modeled vegetation changes induce a regional cooling for the Late Saalian while they cause a slight regional warming for LGM. As a result, ablation along the margins of the Late Saalian ice sheet is significantly reduced, leading to an increased surface mass balance, while there are no significant mass balance changes observed from vegetation feedbacks at LGM.
Patterns of interspecific introgression may vary geographically, and the distribution of introgressed variants can yield insight into the historical dynamics of genetic interactions between hybridizing species. Urodele amphibians, often characterized by limited mobility, deep intraspecific genetic structuring and vulnerability to climatic changes, constitute suitable models for such historical inferences. Here, we combine an extensive survey of the mitochondrial (mtDNA) and nuclear (15 microsatellites) genomes in the Carpathian newt, Lissotriton montandoni (Lm) with species distribution modelling (SDM). Populations of the smooth newt, L. vulgaris (Lv) from the areas surrounding the Lm range were also sampled to test whether gene flow between these hybridizing species extends beyond the area of strict syntopy. The extent of introgression differs dramatically between the mitochondrial genome and the nuclear genome. While multiple, spatially and temporally distinct introgression events from Lv resulted in complete mtDNA replacement in Lm, there was little evidence of recent interspecific nuclear gene flow in the assayed markers. Microsatellite differentiation within Lm defines three units, probably derived from separate glacial refugia, located in the northern, eastern and southern part of the Carpathians. In situ survival and range fragmentation of Lm are supported by SDM, corroborating the role of the Carpathians as a major refugial area. Our results, in combination with previous reports of extensive introgression of the major histocompatibility complex (MHC) genes, emphasize the complexity of historical gene exchange between Lm and Lv.
We analysed 128 mountain hares Lepus timidus varronis from eastern Switzerland with respect to genetic variability, differentiation and phylogeography. The molecular markers chosen were 443 bp of the mitochondrial control region and 13 microsatellite loci (12 of which were polymorphic). Among the 113 successfully sequenced hares, five yielded introgressed brown hare Lepus europaeus haplotypes, making our study one of few to show introgression of mitochondrial brown hare alleles into mountain hare gene pools rather than the other way around. Overall haplotype and nucleotide diversities were 0.91 and 0.0081, and observed and expected heterozygosities were 0.40 and 0.54. Our Swiss sample did not show unequivocal signals of substructuring and probably represents a (nearly) pan-mictic population. We also analysed the 20 haplotypes we found phylogeographically in a global framework by adding 143 published sequences from throughout the species' distribution range. The resulting haplotype network lacked an overall geographical structure, but instead consisted of many geographically meaningful subclusters that were scattered throughout the network, including different groups of Russian, Scandinavian or Alpine sequences. This pattern is in line with earlier findings and expectations for arctic species and is indicative of a continuous population across the European continent during the last ice age. Unexpectedly, our Swiss haplotypes all clustered together, suggesting that most of them originated in situ after the isolation of the Alpine population in the late Pleistocene.
ABSTRACT We review current knowledge of the evolutionary relationships among species of Leporidae drawing on molecular, cytogenetic and morphological data. We highlight problems associated with retrieving phylogenetic information under conditions of a rapid radiation and the lack of phylogenetically informative cytogenetic and mitochondrial DNA characters. Most morphological features underpinning generic distinctions are subtle and prone to reversal and convergence and as a consequence, they generally provide little basis for assessing phylogenetic affinity. We report the results of a supermatrix analysis that combines published nucleotide sequence data, unique insertion/deletion events, morphological characters and presumed geographical centres of origin of each genus. This represents the most comprehensive intergeneric comparison of the Leporidae thus far undertaken. The monophyly of the 11 leporid genera is unambiguously supported. There is support for an Afroasian assemblage that comprises Poelagus, Pronolagus and Nesolagus, a primitive Lepus, with the problematic Bunolagus, Oryctolagus, Caprolagus and Pentalagus as derived species in a clade that also includes the closely related Brachylagus and Sylvilagus as sister taxa. There is no support for the Palaeolaginae, although Romerolagus is an ancient lineage within the extant Leporidae. We hold that of the polytypic genera Lepus remains the most problematic, and provide a working hypothesis that will hopefully encourage future research on the various hare species.
Aim The aim of this paper is to provide a review of the biogeography of the terrestrial mammalian fauna from the Japanese islands.
Location The Japanese archipelago is located off the eastern coast of Asia. It extends over a distance of approximately 2000 km in length, from north to south, and comprises more than 3900 islands of widely differing areas.
Methods The list of the living and Quaternary mammalian fauna of Japan and its geographical distribution was compiled from various published works. Introduced species, marine mammals and bats were not considered in this study. Simpson and Jaccard indices were used to quantify the similarities between the fauna from twelve selected islands from the Japanese archipelago. Regression lines and Pearson correlation coefficients were used to describe the relations between species richness and various geographical factors of the islands, such as area or descriptors of isolation. Lastly, we used the method proposed by Atmar & Patterson (1993) to measure the degree of nestedness of the Japanese terrestrial mammalian fauna.
Results Species richness on islands is highly correlated with island size. However, this study reveals the importance of non‐equilibrium effects. At a large scale, the current distribution of mammals in Japan seems to be due to selective post‐glacial extinction processes. A large proportion of the Japanese mammals are endemic forms, and extinctions were not balanced by the colonization of species from the Asiatic mainland. In addition, we show the major role played by inter‐island dispersal processes, in particular from larger islands towards smaller ones, that are mainly effected by the presence of deep marine channels between islands.
Main conclusions The present distribution of the terrestrial mammalian fauna from Japan is thus mainly the result of post‐glacial extinctions that were not compensated for by colonization of new species from the faunal Asiatic mainland source pool. However, this study emphasizes the importance of inter‐island dispersal processes.
Distribution patterns among the terrestrial mammal species of Sakhalin and the main islands of Japan are shown to fall into 12 clear groups. The most fundamental distributional break (Blakiston's Line) is that separating Hokkaido and Sakhalin to the north, with their boreal fauna typical of northern Eurasia, from ‘Hondo’ (Honshu, Shikoku, Kyushu) to the south, which demonstrates a high degree of endemism and supports a small number of Indo‐Malayan elements. Distribution patterns may be explained by considering the Quaternary geohistory of the area, particularly the formation of land bridges and the changes in climatic conditions during this period. A dynamic classification based upon origin of the fauna recognizes seven categories, although on evidence currently available the allocation of some species to categories is not yet possible.
Hondo underwent two main periods of land bridge connection to the Asiatic mainland. The first, prior to the Pleistocene, allowed immigration of forms which have since developed into distinctive elements of the endemic fauna (‘Old Hondo Endemics’). The second, during the Middle Pleistocene, brought in widespread Palaearctic species as well as components from South‐East Asia (‘Early Colonists’), some of which have since undergone vicariant speciation (‘New Hondo Endemics’); it also allowed several of the Old Hondo Endemics to extend their range to the mainland and Hokkaido (‘Expanding Hondo Endemics’).
Sakhalin and Hokkaido have been more intimately connected to the mainland (most recently until less than 10 000 years ago), such that endemism is very restricted. Species groups here are the ‘Late Colonists’, cold‐adapted tundra species which expanded with the glacial advances, but which are now restricted in distribution, and ‘Recent Colonists’, postglacial forest species which recolonized before the severance of land bridges. Moving the other way were ‘Expanding Northern Endemics’, which arose in Hokkaido or Sakhalin during the last glacial and colonized the adjacent mainland before severance of land links. There are, additionally, several possible Expanding Hondo Endemics in Hokkaido, although human intervention in determining their current distributions cannot be ruled out.
Bats, to which the sea barriers of the Japanese area are less complete, exhibit somewhat different patterns of distribution, confirming predictions about the role of even narrow marine straits in restricting ranges of nonflying mammals.
To investigate genetic diversity among populations of the sika deer, Cervus nippon, nucleotide sequences (705–824 bases) of the mitochondrial D-loop regions were determined in animals from 13 localities in the Japanese islands. Phylogenetic trees constructed by the sequences indicated that the Japanese sika deer is separated into two distinct lineages: the northern Japan group (the Hokkaido island and most of the Honshu mainland) and the southern Japan group (a part of the southern Honshu mainland, the Kyushu island, and small islands around the Kyushu island). All sika deer examined in this study shared four to seven units of repetitive sequences (37 to 40 bases each) within the D-loop sequences. The number of tandem repeats was different among the populations, and it was specific to each population. Six or seven repeats occurred in populations of the northern Japan group, while four or five repeats occurred in populations of the southern Japan group. Each repeat unit included several nucleotide substitutions, compared with others, and 26 types were identified from 31 animals. Sequences of the first, second, and third units in arrays were clearly different between the northern and the southern groups. Based on these D-loop data, colonization and separation of the sika deer populations in the Japanese islands were estimated to have occurred less than 0.5 million years before present. Our results provide an invaluable insight into better understanding the evolutionary history, phylogeny, taxonomy, and population genetics of the sika deer.