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Hibrida vs zona introgresi dalam populasi alami

Hibrida vs zona introgresi dalam populasi alami


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Dalam buku An Introduction to Molecular Ecology, penulis mengatakan bahwa

Introgresi adalah difusi alel dari satu populasi atau spesies ke populasi lain sebagai akibat dari perkawinan silang atau hibridisasi di antara mereka.

Dan hibridisasi itu (kira-kira) perkembangbiakan dua spesies berbeda.

Saya pikir ketika kita berbicara tentang zona introgresi dan zona hibrida, itu adalah hal yang sama.

Tapi inilah interpretasi saya:

Lihat gambar di bawah ini. Di suatu area, Anda akan memiliki 2 populasi dari 2 spesies (A-E). Mereka bisa kawin silang di tengah, ini akan disebut zona hibrida (di C). Namun pergantian alel (atau perpindahan alel) antara dua populasi tidak hanya dilakukan dengan hibridisasi (B vs C). Hal ini dapat dilakukan dengan pembiakan hibrida baru dengan non hibrida (silang balik, dalam B). Kemudian, B ke D akan menjadi zona introgresi.

Saya tidak benar-benar tahu apa yang akan terjadi jika 2 hibrida berkembang biak bersama untuk mendapatkan warna!

Jadi pertanyaan saya adalah: Apa perbedaan antara zona introgresi dan zona hibrida (apakah interpretasi saya benar?)?


Saya pikir Anda benar. Lihat Harrison, R.G. dan E.L. Larson. 2014. Hibridisasi, introgresi, dan sifat spesies. J. Hered. 105: 795-809. Lihat juga https://www.differencebetween.com/difference-between-hybridization-and-vs-introgression/

Menarik bahwa Anda tidak menerima tanggapan untuk ini. Ini pertanyaan yang menarik (dan menurut saya penting).


Struktur genetik zona hibrida antara Silene latifolia dan Silene dioica (Caryophyllaceae): bukti hibridisasi introgresif

Zona hibrida alami menyediakan alat yang berharga untuk mempelajari hibridisasi introgresif, karena mereka dapat berisi berbagai macam genotipe yang dihasilkan dari banyak generasi rekombinasi. Di sini kami menggunakan penanda molekuler dan variasi morfologi untuk menggambarkan struktur dua zona hibrida alami antara Silene latifolia dan Silene dioica di Pegunungan Alpen Swiss. Populasi di kedua zona hibrida terdiri dari beberapa hibrida menengah dan didominasi oleh hibrida silang balik. Yang terakhir ini juga ditemukan pada populasi induk di pinggiran zona hibrida. Dari 209 penanda amplified fragment length polymorphism (AFLP) yang dicetak pada 390 individu, hanya 7 (3,3%) yang spesifik spesies. Hasil ini menunjukkan bahwa introgresi antara S. dioica dan S. latifolia sangat luas, dan zona hibrid bertindak sebagai jembatan untuk aliran gen antara kedua spesies ini. Analisis ketidakseimbangan hubungan mengidentifikasi beberapa populasi di mana hibridisasi sedang berlangsung, sedangkan di sebagian besar populasi, ketidakseimbangan hubungan telah terkikis. Di mana hibridisasi sedang berlangsung, perubahan kuat dalam frekuensi penanda spesifik spesies dan sifat morfologis diamati. Introgresi plastid ke dalam zona hibrida ditemukan dua arah, tetapi hanya haplotipe plastid S. latifolia yang ditemukan di latar belakang S. dioica nuklir. Introgresi plastid searah dari S. latifolia ke S. dioica kemungkinan besar disebabkan oleh aliran polen dari S. dioica ke S. latifolia, dan menghasilkan penangkapan plastid. Perbandingan antara molekul dan indeks hibrida morfologi mengungkapkan bahwa morfologi dalam sistem studi ini berguna untuk mengidentifikasi hibrida, tetapi tidak untuk analisis rinci struktur zona hibrida.


Populasi hibrida secara selektif menyaring introgresi gen antar spesies

Hibrida telah lama dikenal sebagai jalur potensial untuk aliran gen antar spesies yang dapat memiliki konsekuensi penting bagi evolusi dan konservasi biologi. Namun, beberapa penelitian telah menunjukkan bahwa gen dari satu spesies dapat mengintrogresi atau menyerang spesies lain di wilayah geografis yang luas. Menggunakan 35 penanda polimorfisme panjang fragmen restriksi yang dipetakan secara genetik (RFLP) dari dua spesies kayu kapuk (Populus fremontii x P. angustifolia) dan hibridanya (n = 550 pohon), kami menunjukkan bahwa mayoritas genom dilarang melakukan introgressing dari satu spesies ke yang lain. Namun, penghalang ini tidak mutlak Fremont cpDNA dan mtDNA ditemukan di seluruh rentang geografis kayu kapuk berdaun sempit, dan 20% penanda nuklir kapuk Fremont menembus jarak yang bervariasi (beberapa lebih dari 100 km) ke dalam jangkauan spesies penerima. Tingkat introgresi nukleus bervariasi, tetapi dua penanda nukleus mengalami introgresi secepat penanda haploid, kloroplas dan mitokondria yang diturunkan secara sitoplasma. Analisis seluruh genom kami memberikan bukti untuk efek positif, negatif, dan netral dari introgresi. Misalnya, kami memperkirakan bahwa fragmen DNA yang masuk melalui beberapa generasi persilangan balik akan berukuran kecil, karena fragmen kecil cenderung tidak mengandung gen yang merusak. Hasil ini berpendapat bahwa rekombinasi akan menjadi penting, bahwa introgresi bisa sangat selektif, dan bahwa kekuatan evolusioner dalam populasi hibrida untuk secara efektif "menyaring" aliran gen antar spesies. Filter yang kuat dapat membuat introgresi adaptif, mencegah asimilasi genetik, menyebabkan mekanisme isolasi yang santai, dan berkontribusi pada stabilitas zona hibrida. Jadi, alih-alih hibridisasi menjadi faktor negatif seperti yang umumnya diperdebatkan, hibridisasi alami antara spesies asli dapat memberikan variasi genetik penting yang berdampak pada proses ekologi dan evolusi. Akhirnya, kami mengusulkan dua hipotesis yang membedakan kemungkinan introgresi kontemporer versus introgresi kuno dalam sistem ini.


Pengantar

Pendekatan genom memungkinkan wawasan yang semakin dalam tentang kekuatan yang membentuk evolusi genom dalam populasi. Meskipun terbukti bahwa evolusi genom bergantung pada keseimbangan mutasi, evolusi netral, seleksi negatif dan adaptasi, kepentingan relatif dari masing-masing parameter ini masih hanya sebagian yang dipahami. Pemindaian genom sistematis untuk sapuan selektif telah menunjukkan bahwa lokus di bawah seleksi positif baru-baru ini dapat dengan mudah dideteksi pada populasi alami, tetapi juga tanda tangan sapuan dapat dihasilkan melalui efek penyimpangan yang terkait dengan kemacetan populasi atau faktor demografis lainnya [1], [2]. Oleh karena itu sejumlah prosedur statistik yang lebih halus kini telah dikembangkan yang memungkinkan lebih baik membedakan seleksi positif dari efek drift [3]–[6]. Dalam kombinasi dengan data genom densitas tinggi, dengan demikian dimungkinkan untuk mendapatkan wawasan yang lebih dalam tentang dampak seleksi positif pada evolusi genom.

Faktor lain yang meningkatkan relevansi untuk memahami komposisi genetik populasi alami adalah introgresi alelik dari subspesies lain atau spesies yang berkerabat dekat. Meskipun diketahui bahwa hibridisasi antara populasi dan spesies yang berbeda relevan untuk evolusi banyak spesies tumbuhan, kesadaran bahwa proses serupa sedang berlangsung pada populasi hewan baru muncul belakangan ini [7]–[10]. Sementara beberapa contoh spesiasi hibrida pada hewan sekarang telah dijelaskan, masih ada sedikit contoh introgresi wilayah kromosom tertentu [11]–[14]. Bukti bahwa daerah kromosom introgresi berperan dalam adaptasi masih bersifat anekdot dan melibatkan seleksi yang kuat seperti dalam kasus resistensi warfarin pada tikus [13] atau sinyal pilihan pasangan langsung pada kupu-kupu [14].

Kami menggunakan populasi alami tikus rumah (otot) untuk mempelajari genetika adaptasi [15]–[17]. Berasal dari Asia, beberapa spesies dan subspesies tikus telah berevolusi dalam genus Mus dalam jutaan tahun terakhir [18]–. M. m. domesticus dan M. m. otot telah terpisah sekitar 300.000–500.000 tahun yang lalu, yang mencerminkan dalam jumlah generasi dan divergensi molekuler relatif pemisahan simpanse dan manusia. Namun, mereka masih dianggap subspesies, karena mereka dapat disilangkan dan tidak hidup bersimpati. Di sisi lain, jantan hibrida seringkali mandul [21], [22], membuat beberapa penulis menganggap mereka sebagai spesies terpisah [19].

Tikus rumah telah menyebar ke seluruh dunia dan hidup di habitat yang beragam. Sebagai komensal manusia, mereka juga telah menyebar dalam konteks pengembangan pertanian manusia di Eropa dan Asia dalam beberapa ribu tahun terakhir, diikuti oleh kolonisasi seluruh dunia setelah pelayaran lintas benua dalam beberapa ratus tahun terakhir [ 18].

Untuk penelitian ini, kami menggunakan dua populasi alami masing-masing dari M. m. domesticus dan M. m. otot (Gambar 1). keduanya M. m. domesticus populasi berasal dari Perancis Selatan (Fra) dan Jerman Barat (Ger) dan berasal dari gelombang kolonisasi Eropa Barat mulai sekitar 3.000 tahun yang lalu [23]. Sejarah demografis keduanya M. m. otot populasi dari Republik Ceko (Cze) dan Kazakhstan (Kaz) lebih tua tetapi kemungkinan besar masih dalam kerangka waktu ekspansi pertanian manusia [24].

M. m. domesticus terjadi di Eropa Barat, M. m. otot di Eropa Timur dan Asia. Garis merah putus-putus menandai wilayah kontak di mana zona hibrida klasik telah terbentuk. Sampel berasal dari Prancis (Fra – wilayah Massif Central), Jerman (Ger – wilayah Cologne/Bonn), Republik Ceko (Cze – wilayah Studenec) dan Kazhakstan (Kaz – wilayah Almaty, perhatikan bahwa ini tidak ada di peta lagi, seperti yang ditunjukkan oleh panah). Inset menggambarkan hubungan filogenetik antara populasi, serta indikasi parameter yang digunakan untuk pemodelan populasi. Gambar peta berdasarkan peta dari http://d-maps.com.

Kami menggunakan Array Genotipe Keragaman Tikus Affymetrix [25] untuk genotipe individu yang ditangkap secara liar dari populasi masing-masing. Array ini dirancang untuk menutupi variasi untuk M. m. domesticus dan M. m. otot karena mereka adalah subspesies utama yang relevan untuk galur laboratorium tikus rumah. Namun, kami menemukan dalam analisis kami bahwa memanggil SNP di M. m. otot tampaknya kurang dapat diandalkan dan oleh karena itu kami telah menyempurnakan pendekatan statistik untuk mengambil panggilan genotipe yang dapat diandalkan. Kami menggunakan data ini untuk menerapkan sejumlah prosedur statistik untuk mendeteksi seleksi positif di mana setiap prosedur memiliki kelebihan dan masalah untuk layar tersebut. Data kami dari layar lebar genom yang sistematis untuk daerah yang diintrogresi memberikan wawasan baru yang besar tentang frekuensi introgresi daerah kromosom di antara populasi tertentu. Untuk menguji apakah frekuensi yang diamati dari daerah yang diintrogresi dalam suatu populasi serta panjangnya dapat dijelaskan dengan proses netral saja, kami membandingkan hasil kami dengan simulasi koalesen yang menguji parameter migrasi yang berbeda dan menyarankan bahwa keduanya, sapuan selektif yang disebabkan oleh alel langka atau mutasi baru , serta introgresi adaptif haplotipe membentuk komposisi genom tikus.


Hibridisasi vs Introgresi

Hibridisasi dan introgresi adalah dua konsep utama yang mampu membuat keajaiban dalam studi genetik, filogenetik dan evolusi, karena mengarah pada kepunahan genetik dan genotipe dan fenotipe baru. Hibridisasi adalah proses kawin silang antara dua individu yang berbeda secara genetik sedangkan introgresi adalah proses di mana individu dari populasi yang sama kawin silang dan mengalami persilangan balik dengan salah satu atau kedua orang tua. Inilah perbedaan antara hibridisasi dan introgresi.

Referensi:

1. Harrison, Richard G., dan Erica L. Larson. “Hibridisasi, Introgresi, dan Sifat Batas Spesies | Jurnal Keturunan | Akademik Oxford.” Akademik OUP, Oxford University Press, 22 Agustus 2014. Tersedia di sini


Pola introgresi alami dalam a Nothofagus zona hibrida dari hutan beriklim Amerika Selatan

Aliran gen interspesifik adalah fenomena umum di Nothofagaceae spesies bagaimanapun, dinamika introgresi di zona hibrida sebagian besar masih belum diketahui. Kami fokus pada dua yang berbeda secara ekologis dan morfologis Nothofagus spesies dari Patagonia, Nothofagus nervosa dan Nothofagus miring. Di zona hibrida alami, kami membuat dua plot dengan jarak 280 m di ketinggian (sekitar 1,9 °C perbedaan suhu rata-rata), dan dua subplot yang menangkap variasi microsite (kelimpahan dan distribusi spasial spesies dan dominasi arah angin). Kami menggunakan pengambilan sampel intensif individu (2055, termasuk orang dewasa dan regenerasi) dan genotipe molekuler dari 6 mikrosatelit nuklir yang sangat spesifik spesies untuk identifikasi dan klasifikasi hibrida, berdasarkan perkiraan heterozigositas leluhur dan antar kelas. Kami mengevaluasi kontribusi relatif dari efek pengambilan sampel kami terhadap variasi dalam insiden hibrida dan arah introgresi menggunakan model efek campuran linier umum. Kami menentukan bahwa hibridisasi introgresif terjadi pada tingkat global 7,8% dan variasi itu sebagian besar dijelaskan oleh plot (frekuensi di ketinggian rendah kira-kira dua kali lipat ditemukan di ketinggian tinggi), sementara itu kurang dipengaruhi oleh subplot. Plot dataran tinggi didominasi oleh persilangan balik generasi akhir ke n. miring (bimodality asimetris), sedangkan plot ketinggian rendah terdiri dari hibrida menengah (unimodality) dan menunjukkan asimetri untuk introgresi antara subplot. Perbedaan tidak terdeteksi antara orang dewasa dan regenerasi, menunjukkan hambatan isolasi reproduksi kerja awal. Hibrida F1 terjadi pada frekuensi global 3,8%, dan subur, seperti yang ditunjukkan oleh deteksi hibrida generasi pertama dan akhir.

Ini adalah pratinjau konten langganan, akses melalui institusi Anda.


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Hibrida vs zona introgresi dalam populasi alami - Biologi

Zona hibrida dapat dipantau untuk memahami perubahan dalam distribusi spesies.

Zona hibrida dapat dipantau untuk mendokumentasikan introgresi adaptif.

Ilmu warga dapat membantu kami memantau zona hibrida.

Zona hibrida dapat bertindak sebagai jendela perubahan iklim.

Mendefinisikan dampak perubahan iklim antropogenik pada keanekaragaman hayati dan distribusi spesies saat ini menjadi prioritas utama. Model niche berfokus terutama pada perubahan yang diprediksi dalam faktor abiotik, namun interaksi spesies dan evolusi adaptif akan berdampak pada kemampuan spesies untuk bertahan dalam menghadapi perubahan iklim. Tinjauan kami berfokus pada penggunaan zona hibrida untuk memantau respons spesies terhadap perubahan iklim kontemporer. Pemantauan zona hibrida memberikan wawasan tentang bagaimana batas rentang bergeser sebagai respons terhadap perubahan iklim dengan menerangi efek gabungan dari interaksi spesies dan sensitivitas fisiologis. Pada saat yang sama, sifat batas spesies yang semipermeabel memungkinkan kita untuk mendokumentasikan introgresi adaptif alel yang terkait dengan respons terhadap perubahan iklim.


Zona Hibrida dan Proses Evolusi.

Zona hibrida memasuki literatur evolusi melalui sistematika, karena tantangan yang mereka berikan kepada mereka yang ingin spesies mereka dibatasi dengan jelas. Pola variasi dalam zona hibrid adalah salah satu faktor penting yang mengarahkan para ahli sistematika yang tertarik pada proses evolusi untuk mengartikulasikan konsep spesies biologis dan untuk mengembangkan argumen tentang keberadaan spesiasi alopatrik, koadaptasi kumpulan gen spesies, dan asal usul dan spesiasi alopatrik. sifat isolasi reproduksi (Mei 1963). Baru-baru ini, zona hibrida telah berfungsi sebagai "jendela proses evolusi" (Harrison 1990), memberikan kesempatan untuk mempelajari efek aliran gen, keterkaitan, dan beberapa bentuk seleksi pada dinamika genetik.

Apa yang harus kita harapkan untuk dipelajari dari mempelajari zona hibrida? Kita mungkin mengharapkan wawasan tentang beberapa pertanyaan tradisional tentang spesiasi: apakah itu terjadi tidak hanya oleh divergensi alopatrik tetapi juga oleh salah satu dari beberapa proses parapatrik apakah hambatan reproduksi prazigotik berevolusi sebagai respons terhadap seleksi untuk isolasi apa sifat perbedaan genetik di antara spesies, dan mengapa perbedaan berkembang apa hasil mungkin dari kontak antara spesies dalam status nascendi. Kita mungkin menggunakannya untuk belajar tentang epistasis, dan faktor-faktor yang menyebabkan perbedaan populasi. Dan ada pertanyaan tentang zona hibrida dalam hak mereka sendiri: Apakah mereka bergerak? Apakah mereka lokus variasi genetik baru? Apakah hibridisasi mentransfer adaptasi antar spesies, memunculkan adaptasi baru, atau memunculkan spesies baru?

Ini adalah beberapa pertanyaan yang diajukan oleh penulis dari dua belas bab buku ini, yang empat di antaranya mengulas masalah konseptual dan delapan menggambarkan studi kasus. As the editor, Richard Harrison, points out, the study of hybrid zones has been invigorated by new theory and new techniques, especially the use of molecular markers, so that hybrid zones are now seen to be much more complex, and much richer in problems, than they seemed not long ago. The variety of topics and information in this book, consequently, is so great that we must focus our review on a few issues that we find particularly interesting. Throughout, we use Harrison's broad definition: Hybrid zones occur when genetically distinct groups of individuals meet and mate, resulting in at least some offspring of mixed ancestry.

Hybrid Zones and Speciation

Studies of hybrid zones and of speciation are intimately related. Traditionally, "primary" and "secondary" zones have been conceptually distinguished and attributed respectively to differentiation in situ versus secondary contact of populations that differentiated in allopatry. Secondary zones have been identified by multiple concordant clines (including those for presumably neutral markers), and the prevalence of such concordance is one of the traditional arguments for the ubiquity of allopatric speciation (Mayr 1963). It has been argued, however, that primary and secondary zones cannot reliably be distinguished because, inter alia, clines are "attracted" to regions of low density or other interruptions of gene flow, are attracted to each other because of linkage disequilibrium, and create a barrier to the flow even of neutral alleles (Endler 1977 Barton 1983).

In this volume, Mallet most vehemently cites these difficulties and contends that "we do not know the relative likelihood of different modes of speciation, and so it does not seem sensible to accept either [the allopatric or parapatric] model as a null hypothesis" (p. 244). He advocates parapatric speciation, using as a model the Mullerian mimic races of Heliconius butterflies, in which positive frequency-dependent selection creates narrow hybrid belts. Citing evidence against origin of these races in the much-debated Amazonian Pleistocene refugia, Mallet proposes that a new color pattern is fixed in a deme by a peak shift and then spreads by interdemic selection owing to differential deme productivity - that is, by Wright's shifting-balance process. A skeptic might note that this aspect of the shifting-balance theory is strongly debated (Crow et al. 1990, Barton 1992), that it depends on undocumented differences in productivity, and that fixation by a peak shift in a deme is an effectively allopatric process (since it requires low gene flow into the deme note that allopatry and parapatry are a continuum, measured by the migration parameter). Peak shifts between color patterns may be feasible in small demes, since the patterns are subject to positive frequency-dependent selection and there may also be selection against intermediate color patterns, which are generally determined by several gene differences. Nevertheless, mass selection for new patterns could occur if the relative abundance of different model (co-mimic) species changed substantially. Whatever the validity of Haffer's (1969) putative Amazonian refugia might be, we are not convinced by Mallet's dismissal of the possibility that the distribution of Heliconius color patterns can be explained by factors such as spatial variation in the frequency of different co-mimics or different predators. Mallet generalizes from Heliconius raciation to underdominant chromosomes and epistatic gene combinations, arguing that the shifting-balance model could equally well cause parapatric speciation by such substitutions. But unless spread of a new combination is halted by incompatibility with another new, equally fit combination spreading from another focus, interdemic selection of the kind Mallet envisions will simply alter the character of the entire species, rather than generate two species from one. Multiple origins of superior new combinations are of course possible (and are suggested by some chromosome patterns described in Searle's chapter), but they do add a burden to an already rather unparsimonious hypothesis.

Despite the supposed difficulty of distinguishing primary from secondary hybrid zones, several of the authors in this book (e.g., Barton and Gale, Szymura, Hewitt, Patton, Searle) interpret many of their hybrid zones as products of secondary contact, citing diverse reasons for this conclusion, such as Pleistocene history and the location of the zone (Hewitt), the variety of habitats over which each taxon is distributed (Patton), and the multiple chromosomal and genic differences that together reduce hybrid fertility and are unlikely to have formed concordant clines in a continuous population (Searle). To these criteria might be added phylogeographic patterns such as those described for several taxa in southeastern North America (Bermingham and Avise 1986), in which whole clades of haplotypes meet at a hybrid zone. Hybrid zones may retard diffusion of neutral markers, but if they do so for only a few thousand generations as Barton and Gale estimate for the Bombina (fire-bellied toad) hybrid zone, then this will often be insufficient time for monophyletic clades of genes to develop on either side of the zone, and a history of spread from relatively small isolated populations will often be a more plausible interpretation. A review of the kinds of evidence that might distinguish primary from secondary zones, and therefore clarify the origin of incipient species, would have been a useful addition to this book.

Several authors discuss data that can shed light on the genetic basis of reproductive (especially postzygotic) isolation. Szymura describes data on the Bombina hybrid zone, and Barton and Gale summarize the theoretical analysis leading to the estimate that perhaps 55 effective loci contribute to the lower fitness of Bombina hybrids. Searle reviews chromosome hybrid zones in mammals, in a chapter that may be a revelation to those who (like us) only superficially understand karyotype evolution. Many rearrangements have surprisingly little effect on heterokaryotype fertility, or fail to lower fertility in natural populations even when similar rearrangements do so that have arisen in laboratory stocks. Multiple rearrangement differences, however, often do pose substantial barriers to gene flow. Independently segregating rearrangements form coincident clines in some cases, which Searle interprets as instances of secondary contact but in Sorex shrews and some other examples, they are spatially staggered and thus provide little impedance to gene flow. Searle argues that natural selection against multiple heterozygotes may separate the clines, citing as evidence hybrid zones dominated by a homozygous karyotype different from those of the hybridizing races. Both Searle and Shaw et al. emphasize the difficulty of separating the effects of structural rearrangement and gene differences on postzygotic isolation and suggest that both contribute in most cases. Experimental studies of polyploidy in plants, however, have resolved several cases, and in this book, Shaw et al. describe a clever analysis of a most unusual hybrid zone in the grasshopper Caledia captiva, from which they attribute 42% of [F.sub.2] inviability to recombination in the hybrid progeny of chromosomally different but genically equivalent populations. The contribution of chromosomal rearrangements to postzygotic isolation is a controversial issue, at least for animals (White 1978 Coyne et al. 1991 King 1993 Coyne 1994), that may not be resolved for some time.

The possible fates of hybrid zone are many and are related to both the causes of hybrid zones and their evolutionary consequences. They may move, as Shaw et al. demonstrate in Caledia. They may break down more or less in situ, owing to neutral introgression or, as described by Rieseberg and Wendel and by Searle, to selection of alleles that ameliorate hybrid unfitness. One potential fate of particular interest is the long-debated possibility of reinforcement of prezygotic isolation between partially isolated populations, completing the process of speciation. Howard surveys the relevant literature and finds abundant evidence of patterns of reproductive character displacement, but convincing evidence of the process of reinforcement in only four cases. In many instances, however, the evidence on reinforcement is only incomplete, not contrary, and Howard concludes that reinforcement may be more credible than many authors have argued. He attempts to dispatch nine theoretical objections to reinforcement with, we believe, mixed success. For example, we agree that there is little force to the argument that genetic variation for assortative mating will be unavailable, for abundant experimental evidence contradicts this supposition (Rice and Hostert 1993). But Howard perhaps underestimates the force of the argument that recombination dissociates genes that contribute to assortative mating and to hybrid unfitness (Sanderson 1989), an argument that, as Howard notes, applies also to some models of sympatric speciation. This and other theoretical problems to which Howard makes at least some concession may make the compound probability of reinforcement quite low indeed. Nonetheless, Howard may well be right in suggesting that reinforcement appeals to evolutionary biologists not because it justifies preconceived ideas on the nature of species, but because it seems to explain patterns they find in nature.

Botanists, and occasionally zoologists, have suggested that hybrid zones may evolve into stabilized, genetically distinctive populations or even species. Arnold and Bennett present strong molecular evidence of the hybrid origin of a species of Iris, as do Rieseberg and Wendel for three species of Helianthus (sunflower). The latter authors, in a richly informative review of introgression in plants, also consider and come to only tentative conclusions about whether hybridization transfers adaptations between species, and whether it is a source of novel adaptations. The stabilized hybrid species of sunflowers studied by Rieseberg and coworkers have novel habitat associations, suggesting that hybridization may indeed give rise not only to new taxa but also to new adaptations. This outcome of hybridization, which has also been suggested for allopolyploidy (Stebbins 1950 Levin 1983), may have macroevolutionary consequences that deserve exploration with the growing array of molecular techniques.

Stability and Analysis of Hybrid Zones

Hybrid zones may be stable or unstable with respect to position and with respect to genetic dynamics (a distinction that is rarely made explicit in the hybrid-zone literature). In a number of intriguing cases, narrow hybrid zones are thought to have persisted for thousands of years, usually on the assumption that contact between populations isolated in Pleistocene refugia occurred soon after the retreat of the most recent ice sheet. However, evidence is rarely presented that contact was immediately postglacial, rather than much more recent. Hewitt supports this assumption for a Chorthippus grasshopper hybrid zone in the Pyrenees by noting, among other points, that the hybrid zone maps very precisely along the tops of the mountains, as this scenario predicts. Another notable example of a clearly stated justification for this assumption is Meise's (1928) early, careful analysis of the famous hybrid zone between hooded and carrion crows (Corvus) that is about 10 km wide and runs through Scotland and central Europe (figured in Mayr 1963, p. 370). Based on crow fossils from an archeological site in southern Norway, judged to be about 8000 yr old, and on the existence of the hybrid zone in Scotland, which he plausibly supposed was formed before Britain was separated from the continent 8000-9000 yr ago, Meise concluded that the hybrid zone was at least 8000 yr old. He proposed that these generalized birds expanded northward at the same rate as did their forest habitats. This is surely a reasonable supposition for many species. Meise had little direct evidence on the rate of postglacial forest expansion, but more recent evidence indicates lags of less than 3000 yr between glacial retreat and reforestation, although, to be sure, species move at different rates (Pielou 1991).

Even if contact were initiated thousands of years ago, of course, it is possible that the breakdown of reproductive isolation is more recent. Nevertheless, Mayr (1942, 1963) cited the duration of the hybrid zones in Corvus and other taxa as evidence both for genetic coadaptation and against reinforcement of prezygotic isolation. In recent decades, much attention has been directed toward developing explicit models to explain how stable hybrid zones might be maintained. Theoretically, hybrid-zone stability may result from hybrids being (1) less fit as a consequence of their interactions with their environment, (2) more fit than parental genotypes in an intermediate or novel environment, with clines following a gradient in selection coefficients, or (3) intrinsically less fit than "pure" individuals because of genetic incompatibilities, without an ecological component to selection. In (2), hybrid-zone maintenance depends only on selection, independent of dispersal, whereas (1) and (3) involve a balance between selection and dispersal. Moore and Price provide the useful terms "exogenous" selection for (1) and (2) and "endogenous" selection for (3). In recent years, most efforts to explain apparent stability of hybrid zones have focused on (3), a dynamic equilibrium model based on endogenous hybrid inferiority. Hybrid zones of this sort are known as "tension zones" (Key 1968, Barton and Hewitt 1985) and have been the subject of extensive theoretical and modeling work by Barton and colleagues (summarized in this book by Barton and Gale).

Interestingly, although exogenous selection has been cited as a factor that makes it difficult to distinguish primary from secondary zones, the majority of hybrid zones described in this volume are attributed to endogenous selection (indeed, Barton and Hewitt [1985, 1989] have argued that most hybrid zones that have been identified are tension zones). For example, Shaw et al. report complete inviability of [F.sub.2]s and partial inviability of backcrosses in hybridizing Caledia grasshoppers, and Hewitt and colleagues have found that when two Chorthippus grasshoppers are crossed, [F.sub.1] males show severe testis dysfunction and are sterile. Exogenous selection may be more difficult to demonstrate, but is invoked by Moore and Price to explain a hybrid zone in flickers (Colaptes), based on its concordance with climatic variables and the distributions of other organisms by Arnold and Bennett (also see Cruzan and Arnold 1993), who cite both greenhouse data on shade tolerance and the habitat distributions of parental and hybrid irises (Iris) and by Mallet, who describes the Mullerian mimic races of Heliconius butterflies. The Heliconius case, in which narrow contact zones are maintained by positive frequency-dependent selection (resulting from predation by birds) is unusual in that it has the dynamics of a tension zone but is maintained by extrinsic ecological selection. Demonstrating and determining the causes of exogenous selection may require experiments, such as reciprocal transplantation, but almost the only experimentation reported in this book is the work on Iris described by Arnold and Bennett (but see Mallet and Barton [1989] on Heliconius). Clearly, experimentation will be an important complement to the extensive description that has characterized most study of hybrid zones thus far.

Many hybrid zones do not fit neatly into the classification scheme outlined above. For example, Hewitt (1989) has argued that in many cases taxa have probably experienced repeated cycles of range expansion and contraction in conjunction with climatic cycles of cooling and warming. This could result in important differences accumulating through all stages of allopatry, parapatry, and sympatry, blurring the distinction between hybrid zones resulting from primary divergence versus secondary contact. Similarly, some hybrid zones are maintained by a combination of endogenous and exogenous selection. For example, in the Gryllus hybrid zones studied by Rand and Harrison (1989), one of the two reciprocal crosses produces no offspring (endogenous selection), but there also appears to be strong ecological selection for alternate multilocus genotypes in different microhabitats (exogenous selection). A similar situation may hold for the Louisiana irises (Arnold and Bennett, chap. 5 Cruzan and Arnold 1993) and many other systems.

Given this diversity of structure and dynamics, hybrid-zone biologists will turn eagerly for guidance to the chapter by Barton and Gale on "Genetic analysis of hybrid zones", which describes how genotypic and phenotypic patterns in a hybrid zone can be used to draw inferences about the dynamic processes that account for hybrid-zone stability. The authors summarize the techniques developed by Barton and collaborators for analyzing hybrid zones using information on spatial patterns of gene frequencies, linkage disequilibria, and quantitative characters to estimate selection and dispersal parameters. Particularly helpful is their explanation of how to integrate data on discrete characters with quantitative trait data. For field workers, however, this chapter falls somewhat short of the generality implied by its title, because although the techniques are elegant and are shown to be robust in several important ways, the authors do not address the question of precisely when the methodology is appropriate and when it is not. Exactly what are the important assumptions of the models presented here, how generally are they met in nature, and how might we tell? Do dispersal estimates derived from linkage disequilibria depend on assuming a stable state (instead of, say, ongoing completely neutral diffusion) and, if so, how should this assumption be tested? How do details of population structure affect the behavior of the models? How about heterogeneity of population densities or dispersal parameters? What sort of data, and how much, are necessary for meaningful results? Some of these questions are addressed to some degree in the body of the text or in the mathematical appendix, but a more systematically organized "cookbook," with explicitly stated assumptions, would be extremely helpful - perhaps a flow chart to guide the investigator from the first suspicion of hybridization through each step of analysis. If such a general guide is impossible given the diversity and complexity of natural situations, a discussion of why this is so would be very useful.

Real and theoretical hybrid zones will often differ substantially. In some instances, such deviations might be important simply because they lead to inaccurate parameter estimates in other cases, they may indicate fundamental differences from the evolutionary dynamics of the clines described by the models. For example, work in recent years by several researchers (Rand and Harrison 1989 Cruzan and Arnold 1993 Rieseberg and Ellstrand 1993) has led to the recognition that habitats, and associated genotypes, may often be patchily distributed, resulting in a "mosaic" hybrid zone, for which a cline analysis is presumably quite inappropriate (although the question of relevant biological scale is critical here - a mosaic pattern at one scale could be a simple cline at a larger scale). In a still greater departure from standard models, Hewitt suggests that the traditional view of two "fronts" of taxa coming into contact and diffusing into each other following isolation is probably often unrealistic. Rather, it is likely that small numbers of long-distance migrants move beyond the "front lines" and establish populations. Although mixing of alleles associated with heterozygote disadvantage will eventually result in a tension zone with equilibrium dimensions, for neutral alleles, such long-distance colonization can lead to clines considerably broader than expected. Hewitt notes, further, that even in the case of heterozygote disadvantage, if dispersal is low (Nm [less than] 1), colonies of homozygotes established by early pioneers may persist, leading to a fine-scale mosaic. Mallet provides another example of biological realism that might alter the conclusions of an analysis. In discussing what he believes to be moving clines in Heliconius, he suggests that the usual prediction that tension zones will be trapped in areas of low population density hinges on the assumption that dispersal rates are homogeneous across a hybrid zone, whereas in reality dispersal might instead be greater out of regions with low resource density. None of the authors emphasizes the possible role of habitat selection in maintaining the position of animal hybrid zones. This may be a plausible hypothesis for cases such as the flickers, in which a hybrid zone persists despite broad dispersal and no evidence of either assortative mating or reduced reproductive success of hybrids (Moore and Price). Indeed, the genetics of habitat selection in hybrid zones is an intriguing topic that has received almost no attention. In instances such as Bombina, in which parental taxa (and hybrids that resemble them) differ in breeding habitat (Szymura), genetic differences in habitat selection may both retard introgression and at the same time break down because of introgression. Both theoretical and empirical studies of this problem may prove fruitful.

Recent decades have seen major theoretical progress and a remarkable accumulation of data on patterns of variation in particular hybrid zones. On the theoretical front, the major challenge, perhaps, is to expand theory so as to encompass the diversity of situations and rampant heterogeneity that students of hybrid zones find or suspect. Molecular biology has provided an ever-expanding arsenal of analytical techniques, permitting high-resolution descriptions of distribution patterns of molecular markers. Using a combination of uniparentally inherited cytoplasmic and biparentally inherited nuclear markers has proved to be an especially powerful approach for drawing inferences about hybrid-zone dynamics (Arnold 1993). These new tools have both confirmed suspected patterns and provided completely new insights. However, as Rieseberg and Wendel emphasize, it is often very difficult to move beyond mere descriptions of pattern to an understanding of evolutionary processes and mechanisms. For example, although detailed analysis of molecular markers has clearly confirmed the long-held belief that introgression is common in plants, determining the evolutionary importance of this introgression is a more elusive goal. As Rieseberg and Wendel note, such questions will require supplementing molecular descriptions of hybrid zones with ecological studies of populations, including experimental approaches (e.g., reciprocal transplant experiments using parental and recombinant genotypes in different environments, or examination of the effects of introgression on reproductive barriers). Arnold and Bennett describe the beginning of such an integrated program, which may well point the way toward understanding patterns of selection in hybrid zones (also see Arnold and Hedges 1995). As part of such a program, the importance of studying multiple contact zones cannot be overemphasized. By studying the same taxa in different situations, it may be possible to correlate differences in hybrid-zone structure with characteristics such as age, population structure, and congeners present. It appears to us that this approach has been underutilized, although it is of course not an option with every system.

Arbitrarily chosen molecular and morphological markers have provided abundant insights into hybrid zones, but they have not answered some of the most difficult and important questions: on what genes and characters does selection act, and what are the agents of selection? Although Hybrid Zones and the Evolutionary Process provides a fascinating, rich account of the current study of hybrid zones, much of the most important work lies ahead.

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Arnold, M. L., and S. A. Hedges. 1995. Are natural hybrids fit or unfit relative to their parents? Trends in Ecology and Evolution 10:67-71.

Barton, N.H. 1983. Multilocus clines. Evolution 37:454-471.

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Barton, N. H., and G. M. Hewitt. 1985. Analysis of hybrid zones. Annual Review of Ecology and Systematics 16:113-148.

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Crow, J. F., W. R. Engels, and C. Denniston. 1990. Phase three of Wright's shifting-balance theory. Evolution 44:233-247.

Cruzan, M. B., and M. L. Arnold. 1993. Ecological and genetic associations in an Iris hybrid zone. Evolution 47:1432-1445.

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D-statistics for Dummies: A simple test for introgression

Introgressive hybridization seems to be a common phenomenon. The advent of genomic data has revealed the exchange of genetic material between numerous species (see for example Mallet et al. (2016) and Taylor & Larson (2019) for recent reviews). In concert with the explosive expansion in genomic resources, scientists have developed several statistical tests to detect introgression. I have provided an overview of these methods in my Avian Research paper: “Avian Introgression in the Genomic Era”. However, new methods keep popping up and a recent addition to the introgression-toolbox is particularly interesting: in the journal Biologi dan Evolusi Molekuler, Matthew Hahn and Mark Hibbins introduce a three-sample test for introgression.

To understand the rationale behind this test – which has been dubbed D3 – we first have to delve into the D-statistic, also known as the ABBA-BABA-test. This approach was developed to quantify the amount of genetic exchange between Neanderthals and modern humans. The rationale behind this test is quite straightforward: it considers ancestral (‘A’) and derived (‘B’) alleles across the genomes of four taxa. Under the scenario without introgression, two particular allelic patterns ‘ABBA’ and ‘BABA’ should occur equally frequent. An excess of either ABBA or BABA, resulting in a D-statistic that is significantly different from zero, is indicative of gene flow between two taxa. A positive D-statistic (i.e. an excess of ABBA) points to introgression between P2 and P3, whereas a negative D-statistic (i.e. an excess of BABA) points to introgression between P1 and P3.

A Z-score can be calculated to assess the significance of the D-statistic. I will not explain the mathematical underpinnings of the Z-score. All you need to know, is that a Z-score bigger than 3 or smaller than -3 can be interpreted as a significant result. Interested readers can check Durand et al. (2011) for more information.

The figure below illustrates the D-statistic with an example from my own work (see Ottenburghs et al. (2017) for more details). Comparing the genomes of four goose species reveals that Cackling Goose (Branta hutchinsii) and Canada Goose (B. canadensis) share more derived alleles than expected by chance. The resulting positive D-statistic suggests introgression between these species, which is not that surprising because there is a hybrid zone between these geese.

The positive D-statistic indicates an excess of ABBA-patterns in the genomes of these geese, suggesting introgression between Cackling Goose (Branta hutchinsii) and Canada Goose (B. canadensis). Based on Ottenburghs et al. (2017) Biologi Evolusi BMC

Three-sample Test

One limitation of the D-statistic is that you need an outgroup to discriminate between ancestral and derived alleles. The method by Hahn and Hibbins circumvents this issue by focusing on branch lengths instead. Let’s see how this works. Consider a tree with three species: A, B and C. The correct arrangement of these species is shown below: A is more closely related to B than to C. In this case, there are two discordant arrangements: AC and BC. When there is no introgression, these discordance patterns should occur in equal frequencies. With introgression, however, we can expect other patterns. The authors explain that “introgression between B and C leads to both more trees with a BC topology and a shorter pairwise distance between these two lineages. As a result, dB–C [i.e. genetic distance between B and C] will be smaller than dA–C [i.e. genetic distance between A and C], leading to a negative value of D3. Conversely, gene flow between A and C leads to positive values of D3.”

Two discordance arrangements (BC and AC) are expected in equal frequencies when there is no gene flow. With introgression, one pattern becomes more common and results in a decreased genetic distance between some species. From: Hahn & Hibbins (2019) Biologi dan Evolusi Molekuler

Putting it into Practice

From this line of thinking, the researchers deduced a formula (see below) that is solely based on the genetic distances between the species and does not require an outgroup. I applied this new statistic to my goose data. I searched through my PhD-archive and found a table of genetic distances between the different goose species. Putting these numbers into the formula resulted in a D3 of -0.01 This outcome suggests gene flow between B and C, which corresponds to Cackling Goose and Canada Goose. This is in line with my findings based on the D-statistic (luckily…). Unfortunately, I could not test the significance of this result.

Some Cautionary Notes

This new statistic seems promising for studies that could not sample an appropriate outgroup. However, one should not take this method at face value. A significant D3-statistic does not automatically mean that there has been introgression. Other evolutionary processes can influence this statistic (similar to the classic D-statistic). For example, population structure in the ancestor can produce deviations in the number of discordance topologies. Or introgression might come from unsampled or extinct species. Therefore, it is important to complement these statistics with other analyses to quantify introgression.

Durand, E. Y., Patterson, N., Reich, D., & Slatkin, M. (2011). Testing for ancient admixture between closely related populations. Biologi dan Evolusi Molekuler, 28(8), 2239-2252.

Hahn, M. W., & Hibbins, M. S. (2019). A three-sample test for introgression. Molecular Biology and Evolution.

Leafloor, J. O., Moore, J. A., & Scribner, K. T. (2013). A hybrid zone between Canada Geese (Branta canadensis) and Cackling Geese (B. hutchinsii). Auk, 130(3), 487-500.

Mallet, J., Besansky, N., & Hahn, M. W. (2016). How reticulated are species? BioEsai, 38(2), 140-149.

Ottenburghs, J., Megens, H. J., Kraus, R. H., Van Hooft, P., van Wieren, S. E., Crooijmans, R. P., Ydenberg, R.C., Groenen, M.A.M. & Prins, H. H. T. (2017). A history of hybrids? Genomic patterns of introgression in the True Geese. Biologi Evolusi BMC, 17(1), 201.

Ottenburghs, J., Kraus, R. H., van Hooft, P., van Wieren, S. E., Ydenberg, R. C., & Prins, H. H. (2017). Avian introgression in the genomic era. Avian Research, 8(1), 30.

Taylor, S. A., & Larson, E. L. (2019). Insights from genomes into the evolutionary importance and prevalence of hybridization in nature. Nature Ecology & Evolution, 3(2), 170-177.


Tonton videonya: Dinamika Gen Dalam Populasi #TbioUinsu (November 2022).